464 results on '"Chang, DK"'
Search Results
2. CAF hierarchy driven by pancreatic cancer cell p53-status creates a pro-metastatic and chemoresistant environment via perlecan
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Vennin, C, Melenec, P, Rouet, R, Nobis, M, Cazet, As, Murphy, Kj, Herrmann, D, Reed, Da, Lucas, Mc, Warren, Sc, Elgundi, Z, Pinese, M, Kalna, G, Roden, D, Samuel, M, Zaratzian, A, Grey, St, Da Silva, A, Leung, W, Mathivanan, S, Wang, Yx, Braithwaite, Aw, Christ, D, Benda, A, Parkin, A, Phillips, Pa, Whitelock, Jm, Gill, Aj, Sansom, Oj, Croucher, Dr, Parker, Bl, Pajic, M, Morton, Jp, Cox, Tr, Timpson, P, Johns, Al, Chantrill, La, Chou, A, Steinmann, A, Arshi, M, Dwarte, T, Froio, D, Pereira, B, Ritchie, S, Chambers, Cr, Metcalf, X, Waddell, N, Pearson, Jv, Patch, Am, Nones, K, Newell, F, Mukhopadhyay, P, Addala, V, Kazakoff, S, Holmes, O, Leonard, C, Wood, S, Grimmond, Sm, Hofmann, O, Christ, A, Bruxner, T, Samra, Js, Pavlakis, N, High, Ha, Asghari, R, Merrett, Nd, Pavey, D, Das, A, Cosman, Ph, Ismail, K, O'Connnor, C, Stoita, A, Williams, D, Spigellman, A, Lam, Vw, Mcleod, D, Kirk, J, Kench, Jg, Grimison, P, Cooper, Cl, Sandroussi, C, Goodwin, A, Mead, Rs, Tucker, K, Andrews, L, Texler, M, Forest, C, Epari, Kp, Ballal, M, Fletcher, Dr, Mukhedkar, S, Zeps, N, Beilin, M, Feeney, K, Nguyen, Nq, Ruszkiewicz, Ar, Worthley, C, Chen, J, Brooke-Smith, Me, Papangelis, V, Clouston, Ad, Barbour, Ap, O'Rourke, Tj, Fawcett, Jw, Slater, K, Hatzifotis, M, Hodgkinson, P, Nikfarjam, M, Eshleman, Jr, Hruban, Rh, Wolfgang, Cl, Lawlor, Rt, Beghelli, S, Corbo, V, Scardoni, M, Bassi, C, Biankin, Av, Dixon, J, Jamieson, Nb, and Chang, Dk
- Subjects
0301 basic medicine ,medicine.medical_treatment ,Drug Resistance ,General Physics and Astronomy ,02 engineering and technology ,Mice ,Cancer-Associated Fibroblasts ,Cell Movement ,lcsh:Science ,Inbred BALB C ,Cancer ,education.field_of_study ,Mice, Inbred BALB C ,Multidisciplinary ,Tumor ,021001 nanoscience & nanotechnology ,3. Good health ,Gene Expression Regulation, Neoplastic ,medicine.anatomical_structure ,0210 nano-technology ,Pancreas ,Signal Transduction ,Cancer microenvironment ,Cell biology ,Science ,Population ,Perlecan ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Article ,Cell Line ,03 medical and health sciences ,Pancreatic cancer ,Cell Line, Tumor ,medicine ,Humans ,Animals ,Neoplasm Invasiveness ,education ,Cell Proliferation ,Neoplastic ,fungi ,General Chemistry ,Immunotherapy ,medicine.disease ,Pancreatic Neoplasms ,030104 developmental biology ,Gene Expression Regulation ,Drug Resistance, Neoplasm ,Cancer cell ,Cancer research ,biology.protein ,Neoplasm ,lcsh:Q ,Stromal Cells ,Tumor Suppressor Protein p53 ,Heparan Sulfate Proteoglycans - Abstract
Heterogeneous subtypes of cancer-associated fibroblasts (CAFs) coexist within pancreatic cancer tissues and can both promote and restrain disease progression. Here, we interrogate how cancer cells harboring distinct alterations in p53 manipulate CAFs. We reveal the existence of a p53-driven hierarchy, where cancer cells with a gain-of-function (GOF) mutant p53 educate a dominant population of CAFs that establish a pro-metastatic environment for GOF and null p53 cancer cells alike. We also demonstrate that CAFs educated by null p53 cancer cells may be reprogrammed by either GOF mutant p53 cells or their CAFs. We identify perlecan as a key component of this pro-metastatic environment. Using intravital imaging, we observe that these dominant CAFs delay cancer cell response to chemotherapy. Lastly, we reveal that depleting perlecan in the stroma combined with chemotherapy prolongs mouse survival, supporting it as a potential target for anti-stromal therapies in pancreatic cancer., Subtypes of cancer associated fibroblasts can both promote and suppress tumorigenesis. Here, the authors investigate how p53 status in pancreatic cancer cells affects their interaction with cancer associated fibroblasts, and report perlecan as a mediator of the pro-metastatic environment.
- Published
- 2019
3. Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer
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Dreyer, SB, Upstill-Goddard, R, Paulus-Hock, V, Paris, C, Lampraki, EM, Dray, E, Serrels, B, Caligiuri, G, Rebus, S, Plenker, D, Galluzzo, Z, Brunton, H, Cunningham, R, Tesson, M, Nourse, C, Bailey, UM, Jones, MD, Moran-Jones, K, Wright, DW, Duthie, F, Oien, K, Evers, L, McKay, CJ, McGregor, GA, Gulati, A, Brough, R, Bajrami, I, Pettitt, S, Dziubinski, ML, Candido, J, Balkwill, F, Barry, ST, Grützmann, R, Rahib, L, Allison, S, Bailey, PJ, Biankin, AV, Beraldi, D, Cameron, E, Chang, DK, Cooke, SL, Grimwood, P, Kelly, S, Marshall, J, Martin, S, McDade, B, McElroy, D, Musgrove, EA, Ramsay, D, Wright, D, Hair, J, Jamieson, NB, Westwood, P, Williams, N, Johns, AL, Mawson, A, Scarlett, CJ, Brancato, MAL, Rowe, SJ, Simpson, SH, Martyn-Smith, M, Thomas, MT, Chantrill, LA, Chin, VT, Chou, A, Cowley, MJ, Humphris, JL, Mead, RS, Nagrial, AM, Pajic, M, Pettit, J, Pinese, M, Rooman, I, Wu, J, Tao, J, DiPietro, R, Watson, C, Steinmann, A, Lee, HC, Wong, R, Pinho, AV, Giry-Laterriere, M, Daly, RJ, Sutherland, RL, Grimmond, SM, Waddell, N, Kassahn, KS, Miller, DK, Wilson, PJ, Patch, AM, Song, S, Harliwong, I, Idrisoglu, S, Nourbakhsh, E, Manning, S, Wani, S, Gongora, M, Anderson, M, Holmes, O, Leonard, C, Dreyer, SB, Upstill-Goddard, R, Paulus-Hock, V, Paris, C, Lampraki, EM, Dray, E, Serrels, B, Caligiuri, G, Rebus, S, Plenker, D, Galluzzo, Z, Brunton, H, Cunningham, R, Tesson, M, Nourse, C, Bailey, UM, Jones, MD, Moran-Jones, K, Wright, DW, Duthie, F, Oien, K, Evers, L, McKay, CJ, McGregor, GA, Gulati, A, Brough, R, Bajrami, I, Pettitt, S, Dziubinski, ML, Candido, J, Balkwill, F, Barry, ST, Grützmann, R, Rahib, L, Allison, S, Bailey, PJ, Biankin, AV, Beraldi, D, Cameron, E, Chang, DK, Cooke, SL, Grimwood, P, Kelly, S, Marshall, J, Martin, S, McDade, B, McElroy, D, Musgrove, EA, Ramsay, D, Wright, D, Hair, J, Jamieson, NB, Westwood, P, Williams, N, Johns, AL, Mawson, A, Scarlett, CJ, Brancato, MAL, Rowe, SJ, Simpson, SH, Martyn-Smith, M, Thomas, MT, Chantrill, LA, Chin, VT, Chou, A, Cowley, MJ, Humphris, JL, Mead, RS, Nagrial, AM, Pajic, M, Pettit, J, Pinese, M, Rooman, I, Wu, J, Tao, J, DiPietro, R, Watson, C, Steinmann, A, Lee, HC, Wong, R, Pinho, AV, Giry-Laterriere, M, Daly, RJ, Sutherland, RL, Grimmond, SM, Waddell, N, Kassahn, KS, Miller, DK, Wilson, PJ, Patch, AM, Song, S, Harliwong, I, Idrisoglu, S, Nourbakhsh, E, Manning, S, Wani, S, Gongora, M, Anderson, M, Holmes, O, and Leonard, C
- Abstract
Background & Aims: Continuing recalcitrance to therapy cements pancreatic cancer (PC) as the most lethal malignancy, which is set to become the second leading cause of cancer death in our society. The study aim was to investigate the association between DNA damage response (DDR), replication stress, and novel therapeutic response in PC to develop a biomarker-driven therapeutic strategy targeting DDR and replication stress in PC. Methods: We interrogated the transcriptome, genome, proteome, and functional characteristics of 61 novel PC patient–derived cell lines to define novel therapeutic strategies targeting DDR and replication stress. Validation was done in patient-derived xenografts and human PC organoids. Results: Patient-derived cell lines faithfully recapitulate the epithelial component of pancreatic tumors, including previously described molecular subtypes. Biomarkers of DDR deficiency, including a novel signature of homologous recombination deficiency, cosegregates with response to platinum (P <.001) and PARP inhibitor therapy (P <.001) in vitro and in vivo. We generated a novel signature of replication stress that predicts response to ATR (P <.018) and WEE1 inhibitor (P <.029) treatment in both cell lines and human PC organoids. Replication stress was enriched in the squamous subtype of PC (P <.001) but was not associated with DDR deficiency. Conclusions: Replication stress and DDR deficiency are independent of each other, creating opportunities for therapy in DDR-proficient PC and after platinum therapy.
- Published
- 2021
4. ESMO recommendations on predictive biomarker testing for homologous recombination deficiency and PARP inhibitor benefit in ovarian cancer
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Miller, RE, Leary, A, Scott, CL, Serra, V, Lord, CJ, Bowtell, D, Chang, DK, Garsed, DW, Jonkers, J, Ledermann, JA, Nik-Zainal, S, Ray-Coquard, I, Shah, SP, Matias-Guiu, X, Swisher, EM, Yates, LR, Nik-Zainal Abidin, Serena [0000-0001-5054-1727], and Apollo - University of Cambridge Repository
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Ovarian Neoplasms ,homologous recombination deficiency (HRD) ,genomic scar assays ,poly-ADP ribose inhibitors (PARPi) ,BRCA ,Humans ,Female ,Carcinoma, Ovarian Epithelial ,Poly(ADP-ribose) Polymerase Inhibitors ,Homologous Recombination ,Biomarkers - Abstract
BACKGROUND: Homologous recombination repair deficiency (HRD) is a frequent feature of high-grade serous ovarian, fallopian tube and peritoneal carcinoma (HGSC) and is associated with sensitivity to PARP inhibitor (PARPi) therapy. HRD testing provides an opportunity to optimise PARPi use in HGSC but methodologies are diverse and clinical application remains controversial. MATERIALS AND METHODS: To define best practice for HRD testing in HGSC the ESMO Translational Research and Precision Medicine Working Group launched a collaborative project that incorporated a systematic review approach. The main aims were to (i) define the term 'HRD test'; (ii) provide an overview of the biological rationale and the level of evidence supporting currently available HRD tests; (iii) provide recommendations on the clinical utility of HRD tests in clinical management of HGSC. RESULTS: A broad range of repair genes, genomic scars, mutational signatures and functional assays are associated with a history of HRD. Currently, the clinical validity of HRD tests in ovarian cancer is best assessed, not in terms of biological HRD status per se, but in terms of PARPi benefit. Clinical trials evidence supports the use of BRCA mutation testing and two commercially available assays that also incorporate genomic instability for identifying subgroups of HGSCs that derive different magnitudes of benefit from PARPi therapy, albeit with some variation by clinical scenario. These tests can be used to inform treatment selection and scheduling but their use is limited by a failure to consistently identify a subgroup of patients who derive no benefit from PARPis in most studies. Existing tests lack negative predictive value and inadequately address the complex and dynamic nature of the HRD phenotype. CONCLUSIONS: Currently available HRD tests are useful for predicting likely magnitude of benefit from PARPis but better biomarkers are urgently needed to better identify current homologous recombination proficiency status and stratify HGSC management.
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- 2020
- Full Text
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5. Sex differences in oncogenic mutational processes
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Li, CH, Prokopec, SD, Sun, RX, Yousif, F, Schmitz, N, Al-Shahrour, F, Atwal, G, Bailey, PJ, Biankin, AV, Boutros, PC, Campbell, PJ, Chang, DK, Cooke, SL, Deshpande, V, Faltas, BM, Faquin, WC, Garraway, L, Getz, G, Grimmond, SM, Haider, S, Hoadley, KA, Jiao, W, Kaiser, VB, Karlić, R, Kato, M, Kübler, K, Lazar, AJ, Louis, DN, Margolin, A, Martin, S, Nahal-Bose, HK, Nielsen, GP, Nik-Zainal, S, Omberg, L, P’ng, C, Perry, MD, Polak, P, Rheinbay, E, Rubin, MA, Semple, CA, Sgroi, DC, Shibata, T, Siebert, R, Smith, J, Stein, LD, Stobbe, MD, Thai, K, Wright, DW, Wu, CL, Yuan, K, Zhang, J, Aaltonen, LA, Abascal, F, Abeshouse, A, Aburatani, H, Adams, DJ, Agrawal, N, Ahn, KS, Ahn, SM, Aikata, H, Akbani, R, Akdemir, KC, Al-Ahmadie, H, Al-Sedairy, ST, Alawi, M, Albert, M, Aldape, K, Alexandrov, LB, Ally, A, Alsop, K, Alvarez, EG, Amary, F, Amin, SB, Aminou, B, Ammerpohl, O, Anderson, MJ, Ang, Y, Antonello, D, Anur, P, Aparicio, S, Appelbaum, EL, Arai, Y, Aretz, A, Arihiro, K, Ariizumi, SI, Armenia, J, Arnould, L, Asa, S, Assenov, Y, Aukema, S, Auman, JT, Aure, MR, Awadalla, P, Aymerich, M, Bader, GD, Baez-Ortega, A, Li, CH, Prokopec, SD, Sun, RX, Yousif, F, Schmitz, N, Al-Shahrour, F, Atwal, G, Bailey, PJ, Biankin, AV, Boutros, PC, Campbell, PJ, Chang, DK, Cooke, SL, Deshpande, V, Faltas, BM, Faquin, WC, Garraway, L, Getz, G, Grimmond, SM, Haider, S, Hoadley, KA, Jiao, W, Kaiser, VB, Karlić, R, Kato, M, Kübler, K, Lazar, AJ, Louis, DN, Margolin, A, Martin, S, Nahal-Bose, HK, Nielsen, GP, Nik-Zainal, S, Omberg, L, P’ng, C, Perry, MD, Polak, P, Rheinbay, E, Rubin, MA, Semple, CA, Sgroi, DC, Shibata, T, Siebert, R, Smith, J, Stein, LD, Stobbe, MD, Thai, K, Wright, DW, Wu, CL, Yuan, K, Zhang, J, Aaltonen, LA, Abascal, F, Abeshouse, A, Aburatani, H, Adams, DJ, Agrawal, N, Ahn, KS, Ahn, SM, Aikata, H, Akbani, R, Akdemir, KC, Al-Ahmadie, H, Al-Sedairy, ST, Alawi, M, Albert, M, Aldape, K, Alexandrov, LB, Ally, A, Alsop, K, Alvarez, EG, Amary, F, Amin, SB, Aminou, B, Ammerpohl, O, Anderson, MJ, Ang, Y, Antonello, D, Anur, P, Aparicio, S, Appelbaum, EL, Arai, Y, Aretz, A, Arihiro, K, Ariizumi, SI, Armenia, J, Arnould, L, Asa, S, Assenov, Y, Aukema, S, Auman, JT, Aure, MR, Awadalla, P, Aymerich, M, Bader, GD, and Baez-Ortega, A
- Abstract
Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.
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- 2020
6. Precision Oncology in Surgery: Patient Selection for Operable Pancreatic Cancer.
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Dreyer, SB, Pinese, M, Jamieson, NB, Scarlett, CJ, Colvin, EK, Pajic, M, Johns, AL, Humphris, JL, Wu, J, Cowley, MJ, Chou, A, Nagrial, AM, Chantrill, L, Chin, VT, Jones, MD, Moran-Jones, K, Carter, CR, Dickson, EJ, Samra, JS, Merrett, ND, Gill, AJ, Kench, JG, Duthie, F, Miller, DK, Cooke, S, Aust, D, Knösel, T, Rümmele, P, Grützmann, R, Pilarsky, C, Nguyen, NQ, Musgrove, EA, Bailey, PJ, McKay, CJ, Biankin, AV, Chang, DK, Australian Pancreatic Cancer Genome Initiative, Glasgow Precision Oncology Laboratory, Dreyer, SB, Pinese, M, Jamieson, NB, Scarlett, CJ, Colvin, EK, Pajic, M, Johns, AL, Humphris, JL, Wu, J, Cowley, MJ, Chou, A, Nagrial, AM, Chantrill, L, Chin, VT, Jones, MD, Moran-Jones, K, Carter, CR, Dickson, EJ, Samra, JS, Merrett, ND, Gill, AJ, Kench, JG, Duthie, F, Miller, DK, Cooke, S, Aust, D, Knösel, T, Rümmele, P, Grützmann, R, Pilarsky, C, Nguyen, NQ, Musgrove, EA, Bailey, PJ, McKay, CJ, Biankin, AV, Chang, DK, Australian Pancreatic Cancer Genome Initiative, and Glasgow Precision Oncology Laboratory
- Abstract
OBJECTIVE: We aimed to define preoperative clinical and molecular characteristics that would allow better patient selection for operative resection. BACKGROUND: Although we use molecular selection methods for systemic targeted therapies, these principles are not applied to surgical oncology. Improving patient selection is of vital importance for the operative treatment of pancreatic cancer (pancreatic ductal adenocarcinoma). Although surgery is the only chance of long-term survival, 80% still succumb to the disease and approximately 30% die within 1 year, often sooner than those that have unresected local disease. METHOD: In 3 independent pancreatic ductal adenocarcinoma cohorts (total participants = 1184) the relationship between aberrant expression of prometastatic proteins S100A2 and S100A4 and survival was assessed. A preoperative nomogram based on clinical variables available before surgery and expression of these proteins was constructed and compared to traditional measures, and a postoperative nomogram. RESULTS: High expression of either S100A2 or S100A4 was independent poor prognostic factors in a training cohort of 518 participants. These results were validated in 2 independent patient cohorts (Glasgow, n = 198; Germany, n = 468). Aberrant biomarker expression stratified the cohorts into 3 distinct prognostic groups. A preoperative nomogram incorporating S100A2 and S100A4 expression predicted survival and nomograms derived using postoperative clinicopathological variables. CONCLUSIONS: Of those patients with a poor preoperative nomogram score, approximately 50% of patients died within a year of resection. Nomograms have the potential to improve selection for surgery and neoadjuvant therapy, avoiding surgery in aggressive disease, and justifying more extensive resections in biologically favorable disease.
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- 2020
7. OUTCOME OF ENDOSCOPIC BALLOON DILATATION FOR SMALL BOWEL STRICTURES USING SINGLE-BALLOON ENTEROSCOPY IN PATIENTS WITH CROHN'S DISEASE
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Hong, SN, additional, Goh, MJI, additional, Kim, ER, additional, Chang, DK, additional, and Kim, YH, additional
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- 2019
- Full Text
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8. Tailored first-line and second-line CDK4-targeting treatment combinations in mouse models of pancreatic cancer
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Chou, A, Froio, D, Nagrial, AM, Parkin, A, Murphy, KJ, Chin, VT, Wohl, D, Steinmann, A, Stark, R, Drury, A, Walters, SN, Vennin, C, Burgess, A, Pinese, M, Chantrill, LA, Cowley, MJ, Molloy, TJ, Waddell, N, Johns, A, Grimmond, SM, Chang, DK, Biankin, AV, Sansom, OJ, Morton, JP, Grey, ST, Cox, TR, Turchini, J, Samra, J, Clarke, SJ, Timpson, P, Gill, AJ, Pajic, M, Chou, A, Froio, D, Nagrial, AM, Parkin, A, Murphy, KJ, Chin, VT, Wohl, D, Steinmann, A, Stark, R, Drury, A, Walters, SN, Vennin, C, Burgess, A, Pinese, M, Chantrill, LA, Cowley, MJ, Molloy, TJ, Waddell, N, Johns, A, Grimmond, SM, Chang, DK, Biankin, AV, Sansom, OJ, Morton, JP, Grey, ST, Cox, TR, Turchini, J, Samra, J, Clarke, SJ, Timpson, P, Gill, AJ, and Pajic, M
- Abstract
OBJECTIVE: Extensive molecular heterogeneity of pancreatic ductal adenocarcinoma (PDA), few effective therapies and high mortality make this disease a prime model for advancing development of tailored therapies. The p16-cyclin D-cyclin-dependent kinase 4/6-retinoblastoma (RB) protein (CDK4) pathway, regulator of cell proliferation, is deregulated in PDA. Our aim was to develop a novel personalised treatment strategy for PDA based on targeting CDK4. DESIGN: Sensitivity to potent CDK4/6 inhibitor PD-0332991 (palbociclib) was correlated to protein and genomic data in 19 primary patient-derived PDA lines to identify biomarkers of response. In vivo efficacy of PD-0332991 and combination therapies was determined in subcutaneous, intrasplenic and orthotopic tumour models derived from genome-sequenced patient specimens and genetically engineered model. Mechanistically, monotherapy and combination therapy were investigated in the context of tumour cell and extracellular matrix (ECM) signalling. Prognostic relevance of companion biomarker, RB protein, was evaluated and validated in independent PDA patient cohorts (>500 specimens). RESULTS: Subtype-specific in vivo efficacy of PD-0332991-based therapy was for the first time observed at multiple stages of PDA progression: primary tumour growth, recurrence (second-line therapy) and metastatic setting and may potentially be guided by a simple biomarker (RB protein). PD-0332991 significantly disrupted surrounding ECM organisation, leading to increased quiescence, apoptosis, improved chemosensitivity, decreased invasion, metastatic spread and PDA progression in vivo. RB protein is prevalent in primary operable and metastatic PDA and may present a promising predictive biomarker to guide this therapeutic approach. CONCLUSION: This study demonstrates the promise of CDK4 inhibition in PDA over standard therapy when applied in a molecular subtype-specific context.
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- 2018
9. Lost in translation: Returning germline genetic results in genome-scale cancer research
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Johns, AL, McKay, SH, Humphris, JL, Pinese, M, Chantrill, LA, Mead, RS, Tucker, K, Andrews, L, Goodwin, A, Leonard, C, High, HA, Nones, K, Waddell, N, Patch, AM, Merrett, ND, Pavlakis, N, Kassahn, KS, Samra, JS, Miller, DK, Chang, DK, Pajic, M, Pearson, JV, Grimmond, SM, Zeps, N, Gill, AJ, Biankin, AV, Chin, VT, Chou, A, Steinmann, A, Arshi, M, Drury, A, Froio, D, Morgan, A, Timpson, P, Hermann, D, Vennin, C, Warren, S, Wu, J, Pinho, AV, Newell, F, Mukhopadhyay, P, Addala, V, Kazakoff, S, Holmes, O, Wood, S, Xu, C, Hofmann, O, Wilson, PJ, Christ, A, Bruxner, T, Samra, S, Arena, J, Mittal, A, Asghari, R, Pavey, D, Das, A, Cosman, PH, Ismail, K, O'Connnor, C, Williams, D, Spigellman, A, Lam, W, McLeod, D, Nagrial, AM, Kirk, J, James, V, Grimison, P, Cooper, CL, Sandroussi, C, Forest, C, Epari, KP, Ballal, M, Fletcher, DR, Mukhedkar, S, Beilin, M, Feeney, K, Nguyen, NQ, Ruszkiewicz, AR, Worthley, C, Brooke-Smith, ME, Papangelis, V, Clouston, AD, Martin, P, Barbour, AP, O'Rourke, TJ, Fawcett, JW, Slater, K, Hatzifotis, M, Hodgkinson, P, Hruban, RH, Wolfgang, CL, Hodgin, M, Lawlor, RT, Beghelli, S, Corbo, V, Scardoni, M, Bassi, C, Bailey, P, Martin, S, Musgrove, EA, Johns, AL, McKay, SH, Humphris, JL, Pinese, M, Chantrill, LA, Mead, RS, Tucker, K, Andrews, L, Goodwin, A, Leonard, C, High, HA, Nones, K, Waddell, N, Patch, AM, Merrett, ND, Pavlakis, N, Kassahn, KS, Samra, JS, Miller, DK, Chang, DK, Pajic, M, Pearson, JV, Grimmond, SM, Zeps, N, Gill, AJ, Biankin, AV, Chin, VT, Chou, A, Steinmann, A, Arshi, M, Drury, A, Froio, D, Morgan, A, Timpson, P, Hermann, D, Vennin, C, Warren, S, Wu, J, Pinho, AV, Newell, F, Mukhopadhyay, P, Addala, V, Kazakoff, S, Holmes, O, Wood, S, Xu, C, Hofmann, O, Wilson, PJ, Christ, A, Bruxner, T, Samra, S, Arena, J, Mittal, A, Asghari, R, Pavey, D, Das, A, Cosman, PH, Ismail, K, O'Connnor, C, Williams, D, Spigellman, A, Lam, W, McLeod, D, Nagrial, AM, Kirk, J, James, V, Grimison, P, Cooper, CL, Sandroussi, C, Forest, C, Epari, KP, Ballal, M, Fletcher, DR, Mukhedkar, S, Beilin, M, Feeney, K, Nguyen, NQ, Ruszkiewicz, AR, Worthley, C, Brooke-Smith, ME, Papangelis, V, Clouston, AD, Martin, P, Barbour, AP, O'Rourke, TJ, Fawcett, JW, Slater, K, Hatzifotis, M, Hodgkinson, P, Hruban, RH, Wolfgang, CL, Hodgin, M, Lawlor, RT, Beghelli, S, Corbo, V, Scardoni, M, Bassi, C, Bailey, P, Martin, S, and Musgrove, EA
- Abstract
Background: The return of research results (RoR) remains a complex and well-debated issue. Despite the debate, actual data related to the experience of giving individual results back, and the impact these results may have on clinical care and health outcomes, is sorely lacking. Through the work of the Australian Pancreatic Cancer Genome Initiative (APGI) we: (1) delineate the pathway back to the patient where actionable research data were identified; and (2) report the clinical utilisation of individual results returned. Using this experience, we discuss barriers and opportunities associated with a comprehensive process of RoR in large-scale genomic research that may be useful for others developing their own policies. Methods: We performed whole-genome (n = 184) and exome (n = 208) sequencing of matched tumour-normal DNA pairs from 392 patients with sporadic pancreatic cancer (PC) as part of the APGI. We identified pathogenic germline mutations in candidate genes (n = 130) with established predisposition to PC or medium-high penetrance genes with well-defined cancer associated syndromes or phenotypes. Variants from candidate genes were annotated and classified according to international guidelines. Variants were considered actionable if clinical utility was established, with regard to prevention, diagnosis, prognostication and/or therapy. Results: A total of 48,904 germline variants were identified, with 2356 unique variants undergoing annotation and in silico classification. Twenty cases were deemed actionable and were returned via previously described RoR framework, representing an actionable finding rate of 5.1%. Overall, 1.78% of our cohort experienced clinical benefit from RoR. Conclusion: Returning research results within the context of large-scale genomics research is a labour-intensive, highly variable, complex operation. Results that warrant action are not infrequent, but the prevalence of those who experience a clinical difference as a result of returning
- Published
- 2017
10. Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma
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Feigin, ME, Garvin, T, Bailey, P, Waddell, N, Chang, DK, Kelley, DR, Shuai, S, Gallinger, S, McPherson, JD, Grimmond, SM, Khurana, E, Stein, LD, Biankin, AV, Schatz, MC, Tuveson, DA, Feigin, ME, Garvin, T, Bailey, P, Waddell, N, Chang, DK, Kelley, DR, Shuai, S, Gallinger, S, McPherson, JD, Grimmond, SM, Khurana, E, Stein, LD, Biankin, AV, Schatz, MC, and Tuveson, DA
- Abstract
The contributions of coding mutations to tumorigenesis are relatively well known; however, little is known about somatic alterations in noncoding DNA. Here we describe GECCO (Genomic Enrichment Computational Clustering Operation) to analyze somatic noncoding alterations in 308 pancreatic ductal adenocarcinomas (PDAs) and identify commonly mutated regulatory regions. We find recurrent noncoding mutations to be enriched in PDA pathways, including axon guidance and cell adhesion, and newly identified processes, including transcription and homeobox genes. We identified mutations in protein binding sites correlating with differential expression of proximal genes and experimentally validated effects of mutations on expression. We developed an expression modulation score that quantifies the strength of gene regulation imposed by each class of regulatory elements, and found the strongest elements were most frequently mutated, suggesting a selective advantage. Our detailed single-cancer analysis of noncoding alterations identifies regulatory mutations as candidates for diagnostic and prognostic markers, and suggests new mechanisms for tumor evolution.
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- 2017
11. Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT-ROBO, ITGA2 and MET signaling
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Nones, K, Waddell, N, Song, S, Patch, Am, Miller, D, Johns, A, Wu, J, Kassahn, Ks, Wood, D, Bailey, P, Fink, L, Manning, S, Christ, An, Nourse, C, Kazakoff, S, Taylor, D, Leonard, C, Chang, Dk, Jones, Md, Thomas, M, Watson, C, Pinese, M, Cowley, M, Rooman, I, Pajic, M, Butturini, Giovanni, Malpaga, A, Corbo, Vincenzo, Crippa, Stefano, Falconi, M, Zamboni, Giuseppe, Castelli, P, Lawlor, Rita Teresa, Gill, Aj, Scarpa, Aldo, Pearson, Jv, Biankin, Av, Grimmond, Sm, Apgi, Nones, K, Waddell, N, Song, S, Patch, Am, Miller, D, Johns, A, Wu, J, Kassahn, K, Wood, D, Bailey, P, Fink, L, Manning, S, Christ, An, Nourse, C, Kazakoff, S, Taylor, D, Leonard, C, Chang, Dk, Jones, Md, Thomas, M, Watson, C, Pinese, M, Cowley, M, Rooman, I, Pajic, M, Apgi, Butturini, G, Malpaga, A, Corbo, V, Falconi, Massimo, Zamboni, G, Castelli, P, Lawlor, Rt, Gill, Aj, Scarpa, A, Pearson, Jv, Biankin, Av, Grimmond, S. M., Crippa, Stefano, Basic (bio-) Medical Sciences, and Laboratory for Medical and Molecular Oncology
- Subjects
Adult ,Male ,pancreatic cancer ,Integrin alpha2 ,Nerve Tissue Proteins ,Signal transduction ,Epigenesis, Genetic ,axon-guidance ,Transforming Growth Factor beta ,stellate cell activation ,Humans ,RNA, Messenger ,Receptors, Immunologic ,Promoter Regions, Genetic ,Aged ,DNA methylation ,Base Sequence ,SLIT-ROBO pathway ,Gene Expression Profiling ,Pancreatic Stellate Cells ,Pancreatic Ducts ,Membrane Proteins ,cell adhesion ,Sequence Analysis, DNA ,Middle Aged ,Proto-Oncogene Proteins c-met ,SLIT-ROBO pathway, axon-guidance, methylation, pancreatic cancer, stellate cell activation ,Gene Expression Regulation, Neoplastic ,Pancreatic Neoplasms ,Wnt Proteins ,integrins ,Intercellular Signaling Peptides and Proteins ,Female ,methylation ,aged, 80 and over ,Carcinoma, Pancreatic Ductal - Abstract
The importance of epigenetic modifications such as DNA methylation in tumorigenesis is increasingly being appreciated. To define the genome-wide pattern of DNA methylation in pancreatic ductal adenocarcinomas (PDAC), we captured the methylation profiles of 167 untreated resected PDACs and compared them to a panel of 29 adjacent nontransformed pancreata using high-density arrays. A total of 11,634 CpG sites associated with 3,522 genes were significantly differentially methylated (DM) in PDAC and were capable of segregating PDAC from non-malignant pancreas, regardless of tumor cellularity. As expected, PDAC hypermethylation was most prevalent in the 5' region of genes (including the proximal promoter, 5'UTR and CpG islands). Approximately 33% DM genes showed significant inverse correlation with mRNA expression levels. Pathway analysis revealed an enrichment of aberrantly methylated genes involved in key molecular mechanisms important to PDAC: TGF-β, WNT, integrin signaling, cell adhesion, stellate cell activation and axon guidance. Given the recent discovery that SLIT-ROBO mutations play a clinically important role in PDAC, the role of epigenetic perturbation of axon guidance was pursued in more detail. Bisulfite amplicon deep sequencing and qRT-PCR expression analyses confirmed recurrent perturbation of axon guidance pathway genes SLIT2, SLIT3, ROBO1, ROBO3, ITGA2 and MET and suggests epigenetic suppression of SLIT-ROBO signaling and up-regulation of MET and ITGA2 expression. Hypomethylation of MET and ITGA2 correlated with high gene expression, which was associated with poor survival. These data suggest that aberrant methylation plays an important role in pancreatic carcinogenesis affecting core signaling pathways with potential implications for the disease pathophysiology and therapy.
- Published
- 2014
12. Exploiting the neoantigen landscape for immunotherapy of pancreatic ductal adenocarcinoma
- Author
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Bailey, P, Chang, DK, Forget, MA, Lucas, FAS, Alvarez, HA, Haymaker, C, Chattopadhyay, C, Kim, SH, Ekmekcioglu, S, Grimm, EA, Biankin, AV, Hwu, P, Maitra, A, Roszik, J, Bailey, P, Chang, DK, Forget, MA, Lucas, FAS, Alvarez, HA, Haymaker, C, Chattopadhyay, C, Kim, SH, Ekmekcioglu, S, Grimm, EA, Biankin, AV, Hwu, P, Maitra, A, and Roszik, J
- Abstract
© 2016 The Author(s). Immunotherapy approaches for pancreatic ductal adenocarcinoma (PDAC) have met with limited success. It has been postulated that a low mutation load may lead to a paucity of T cells within the tumor microenvironment (TME). However, it is also possible that while neoantigens are present, an effective immune response cannot be generated due to an immune suppressive TME. To discern whether targetable neoantigens exist in PDAC, we performed a comprehensive study using genomic profiles of 221 PDAC cases extracted from public databases. Our findings reveal that: (a) nearly all PDAC samples harbor potentially targetable neoantigens; (b) T cells are present but generally show a reduced activation signature; and (c) markers of efficient antigen presentation are associated with a reduced signature of markers characterizing cytotoxic T cells. These findings suggest that despite the presence of tumor specific neoepitopes, T cell activation is actively suppressed in PDAC. Further, we identify iNOS as a potential mediator of immune suppression that might be actionable using pharmacological avenues.
- Published
- 2016
13. Histomolecular Phenotypes of Adenocarcinoma of the Ampulla of Vater: More Evidence Is Required Reply
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Chang, Dk, Jamieson, Nb, Scarpa, Aldo, Mckay, Cj, and Biankin, Av
- Subjects
Homeodomain Proteins ,Ampulla of Vater ,Adenocarcinoma ,Common Bile Duct Neoplasms ,Female - Published
- 2013
14. RON is not a prognostic marker for resectable pancreatic cancer
- Author
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Tactacan, Carole M, Chang, David K, Cowley, Mark J, Humphrey, Emily S, Jianmin, Wu, Gill, Anthony J, Chou, Angela, Nones, Katia, Grimmond, Sean M, Sutherland, Robert L, Biankin, Andrew V, Daly, Roger J, Biankin, Av, Johns, Al, Mawson, A, Chang, Dk, Scarlett, Cj, Brancato, Ma, Rowe, Sj, Simpson, Sl, Martyn-Smith, M, Chantrill, La, Chin, Vt, Chou, A, Cowley, Mj, Caplan, W, Humphris, Jl, Jones, Md, Mead, R, Nagrial, Am, Pajic, M, Pettit, J, Pinese, M, Rooman, I, Wu, Jun, Daly, Rj, Musgrove, Ea, Sutherland, Rl, Grimmond, Sm, Waddell, N, Kassahn, Ks, Miller, Dk, Wilson, Pj, Patch, Am, Song, S, Harliwong, I, Idrisoglu, S, Nourse, C, Nourbakhsh, E, Manning, S, Wani, S, Gongora, M, Anderson, Michela, Holmes, O, Leonard, C, Taylor, D, Wood, JOHN STEPHAN, Xu, C, Nones, K, Fink, Julika, Christ, A, Bruxner, T, Cloonan, N, Newell, F, Pearson, Jv, Samra, Js, Gill, Aj, Nickpavlakis, Guminski, A, Toon, C, Asghari, R, Merrett, Nd, Pavey, Da, Das, A, Cosman, Ph, Ismail, K, O'Connor, C, Lam, Vw, Mcleod, D, Pleass, Hc, James, V, Kench, Jg, Cooper, Cl, Joseph, D, Sandroussi, C, Crawford, M, Texler, M, Forrest, C, Laycock, A, Epari, Kp, Ballal, M, Fletcher, Dr, Mukhedkar, S, Spry, Na, Deboer, B, Chai, M, Feeney, K, Zeps, N, Beilin, M, Nguyen, Nq, Ruszkiewicz, Ar, Worthley, C, Tan, Cp, Debrencini, T, Chen, J, Brooke-Smith, Me, Papangelis, V, Tang, H, Barbour, Ap, Clouston, Ad, Martin, P, O'Rourke, Tj, Chiang, A, Fawcett, Jw, Slater, K, Yeung, S, Hatzifotis, M, Hodgkinson, P, Christophi, C, Nikfarjam, M, Eshleman, Jr, Hruban, Rh, Maitra, A, Iacobuzio-Donahue, Ca, Schulick, Rd, Wolfgang, Cl, Morgan, Ra, Scarpa, A, Lawlor, Rt, Beghelli, S, Corbo, V, Scardoni, M, Bassi, C, Tempero, Ma., and Basic (bio-) Medical Sciences
- Subjects
Oncology ,Male ,Receptor Protein-Tyrosine Kinases/analysis ,Cancer Research ,Receptor tyrosine kinase ,Kaplan-Meier Estimate ,Surgical oncology ,80 and over ,Prospective cohort study ,Pancreatic Neoplasms/metabolism ,Biomarker ,Gemcitabine ,Chemotherapy ,Adenocarcinoma ,Adult ,Aged ,Aged, 80 and over ,Biomarkers, Tumor ,Blotting, Western ,Female ,Humans ,Immunohistochemistry ,Middle Aged ,Pancreatic Neoplasms ,Prognosis ,Proportional Hazards Models ,Receptor Protein-Tyrosine Kinases ,Tissue Array Analysis ,Tumor ,Blotting ,lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,Adenocarcinoma/metabolism ,CA19-9 ,Western ,Research Article ,medicine.drug ,medicine.medical_specialty ,lcsh:RC254-282 ,Biomarkers, Tumor/analysis ,Breast cancer ,Internal medicine ,Pancreatic cancer ,medicine ,Genetics ,business.industry ,Cancer ,medicine.disease ,business ,aged, 80 and over ,Biomarkers - Abstract
Background The receptor tyrosine kinase RON exhibits increased expression during pancreatic cancer progression and promotes migration, invasion and gemcitabine resistance of pancreatic cancer cells in experimental models. However, the prognostic significance of RON expression in pancreatic cancer is unknown. Methods RON expression was characterized in several large cohorts, including a prospective study, totaling 492 pancreatic cancer patients and relationships with patient outcome and clinico-pathologic variables were assessed. Results RON expression was associated with outcome in a training set, but this was not recapitulated in the validation set, nor was there any association with therapeutic responsiveness in the validation set or the prospective study. Conclusions Although RON is implicated in pancreatic cancer progression in experimental models, and may constitute a therapeutic target, RON expression is not associated with prognosis or therapeutic responsiveness in resected pancreatic cancer.
- Published
- 2012
15. Targeting mTOR dependency in pancreatic cancer
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Morran, DC, Wu, J, Jamieson, NB, Mrowinska, A, Kalna, G, Karim, SA, Au, AYM, Scarlett, CJ, Chang, DK, Pajak, MZ, Oien, KA, McKay, CJ, Carter, CR, Gillen, G, Champion, S, Pimlott, SL, Anderson, KI, Evans, TRJ, Grimmond, SM, Biankin, AV, Sansom, OJ, Morton, JP, Morran, DC, Wu, J, Jamieson, NB, Mrowinska, A, Kalna, G, Karim, SA, Au, AYM, Scarlett, CJ, Chang, DK, Pajak, MZ, Oien, KA, McKay, CJ, Carter, CR, Gillen, G, Champion, S, Pimlott, SL, Anderson, KI, Evans, TRJ, Grimmond, SM, Biankin, AV, Sansom, OJ, and Morton, JP
- Abstract
OBJECTIVE: Pancreatic cancer is a leading cause of cancer-related death in the Western world. Current chemotherapy regimens have modest survival benefit. Thus, novel, effective therapies are required for treatment of this disease. DESIGN: Activating KRAS mutation almost always drives pancreatic tumour initiation, however, deregulation of other potentially druggable pathways promotes tumour progression. PTEN loss leads to acceleration of Kras(G12D)-driven pancreatic ductal adenocarcinoma (PDAC) in mice and these tumours have high levels of mammalian target of rapamycin (mTOR) signalling. To test whether these KRAS PTEN pancreatic tumours show mTOR dependence, we compared response to mTOR inhibition in this model, to the response in another established model of pancreatic cancer, KRAS P53. We also assessed whether there was a subset of pancreatic cancer patients who may respond to mTOR inhibition. RESULTS: We found that tumours in KRAS PTEN mice exhibit a remarkable dependence on mTOR signalling. In these tumours, mTOR inhibition leads to proliferative arrest and even tumour regression. Further, we could measure response using clinically applicable positron emission tomography imaging. Importantly, pancreatic tumours driven by activated KRAS and mutant p53 did not respond to treatment. In human tumours, approximately 20% of cases demonstrated low PTEN expression and a gene expression signature that overlaps with murine KRAS PTEN tumours. CONCLUSIONS: KRAS PTEN tumours are uniquely responsive to mTOR inhibition. Targeted anti-mTOR therapies may offer clinical benefit in subsets of human PDAC selected based on genotype, that are dependent on mTOR signalling. Thus, the genetic signatures of human tumours could be used to direct pancreatic cancer treatment in the future.
- Published
- 2014
16. Returning individual research results for genome sequences of pancreatic cancer
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Johns, AL, Miller, DK, Simpson, SH, Gill, AJ, Kassahn, KS, Humphris, JL, Samra, JS, Tucker, K, Andrews, L, Chang, DK, Waddell, N, Pajic, M, Pearson, JV, Grimmond, SM, Biankin, AV, Zeps, N, Johns, AL, Miller, DK, Simpson, SH, Gill, AJ, Kassahn, KS, Humphris, JL, Samra, JS, Tucker, K, Andrews, L, Chang, DK, Waddell, N, Pajic, M, Pearson, JV, Grimmond, SM, Biankin, AV, and Zeps, N
- Abstract
BACKGROUND: Disclosure of individual results to participants in genomic research is a complex and contentious issue. There are many existing commentaries and opinion pieces on the topic, but little empirical data concerning actual cases describing how individual results have been returned. Thus, the real life risks and benefits of disclosing individual research results to participants are rarely if ever presented as part of this debate. METHODS: The Australian Pancreatic Cancer Genome Initiative (APGI) is an Australian contribution to the International Cancer Genome Consortium (ICGC), that involves prospective sequencing of tumor and normal genomes of study participants with pancreatic cancer in Australia. We present three examples that illustrate different facets of how research results may arise, and how they may be returned to individuals within an ethically defensible and clinically practical framework. This framework includes the necessary elements identified by others including consent, determination of the significance of results and which to return, delineation of the responsibility for communication and the clinical pathway for managing the consequences of returning results. RESULTS: Of 285 recruited patients, we returned results to a total of 25 with no adverse events to date. These included four that were classified as medically actionable, nine as clinically significant and eight that were returned at the request of the treating clinician. Case studies presented depict instances where research results impacted on cancer susceptibility, current treatment and diagnosis, and illustrate key practical challenges of developing an effective framework. CONCLUSIONS: We suggest that return of individual results is both feasible and ethically defensible but only within the context of a robust framework that involves a close relationship between researchers and clinicians.
- Published
- 2014
17. Synoptic reporting improves histopathological assessment of pancreatic resection specimens
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Gill AJ, Biankin AV, Kench JG, for the NSW Pancreatic Network (incl Sitas F), Johns AL, Eckstein R, Samra JS, Kaufman A, Chang DK, Merrett ND, Cosman PH, and Smith RC
- Subjects
Wales ,Research ,Histological Techniques ,Australia ,Pathology,Surgical ,Cancer Control, Survivorship, and Outcomes Research - Resources and Infrastructure ,Pancreaticoduodenectomy ,methods ,Pancreatic Neoplasms ,surgery ,Pancreatectomy ,Cancer Type - Pancreatic Cancer ,Research Design ,standards ,cancer ,Humans ,pathology ,Other ,New South Wales ,Neoplasm Staging - Abstract
AIM: We examined whether introduction of a standardised pancreatic cancer minimum data set improved the reporting of key pathological features across multiple institutions. METHODS: From seven different pathology departments that are members of the New South Wales Pancreatic Cancer Network, 109 free text reports and 68 synoptic reports were compared. RESULTS: AJCC stage could not be inferred from 44% of free text reports, whereas stage was reported in all 68 synoptic reports. In the free text reports 28 different names were used to designate margins. All margins were reported in only 12 (11%) of the free text reports compared with 64 (94%) of the synoptic reports (p = 0.0011). The presence or absence of lymphovascular or perineural invasion was reported in 72 (66%) and 92 (84%) of free text reports, respectively. In contrast, lymphovascular space and perineural invasion were reported in all synoptic reports (p = 0.0011 and p = 0.0058). CONCLUSION: We conclude that synoptic reporting of pancreatic resections without any other intervention increases the information contained within histopathology reports. Therefore, the introduction of minimal data set synoptic reports is a simple and feasible mechanism to immediately improve reporting for pancreatectomy specimens
- Published
- 2009
18. Improving outcomes for operable pancreatic cancer: is access to safer surgery the problem?
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Chang DK, Merrett ND, Biankin AV, and NSW Pancreatic Cancer Network (incl Sitas F)
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Attitude of Health Personnel ,Physician's Practice Patterns ,surgical management ,survival ,Health Services Accessibility ,Treatment - Localised Therapies – Clinical Applications ,methods ,surgery ,Pancreatectomy ,Cancer Type - Pancreatic Cancer ,Humans ,cancer ,Referral and Consultation ,Neoplasm Staging ,Quality of Health Care ,Patient Care Team ,therapy ,Decision Trees ,Australia ,mortality ,Pancreatic Neoplasms ,Treatment Outcome ,Attitude ,Practice Guidelines as Topic ,adverse effects ,Disease Progression ,pathology ,Other ,Guideline Adherence ,Precancerous Conditions ,Carcinoma in Situ - Abstract
Despite advances in the understanding and treatment of pancreatic cancer in the last two decades, there is a persisting nihilistic attitude among clinicians. An alarmingly high rate of under-utilization of surgical management for operable pancreatic cancer was recently reported in the USA, where more than half of patients with stage 1 operable disease and no other contraindications were not offered surgery as therapy, denying this group of patients a 20% chance of long-term survival. These data indicate that a nihilistic attitude among clinicians may be a significant and reversible cause of the persisting high mortality of patients with pancreatic cancer. This article examines the modern management of pancreatic cancer, in particular, the advances in surgical care that have reduced the mortality of pancreatectomy to almost that of colonic resection, and outlines a strategy for improving outcomes for patients with pancreatic cancer now and in the future
- Published
- 2008
19. Clinical and molecular characterization of HER2 amplified-pancreatic cancer
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Chou, A, Waddell, N, Cowley, MJ, Gill, AJ, Chang, DK, Patch, AM, Nones, K, Wu, J, Pinese, M, Johns, AL, Miller, DK, Kassahn, KS, Nagrial, AM, Wasan, H, Goldstein, D, Toon, CW, Chin, V, Chantrill, L, Humphris, J, Mead, RS, Rooman, I, Samra, JS, Pajic, M, Musgrove, EA, Pearson, JV, Morey, AL, Grimmond, SM, Biankin, AV, Chou, A, Waddell, N, Cowley, MJ, Gill, AJ, Chang, DK, Patch, AM, Nones, K, Wu, J, Pinese, M, Johns, AL, Miller, DK, Kassahn, KS, Nagrial, AM, Wasan, H, Goldstein, D, Toon, CW, Chin, V, Chantrill, L, Humphris, J, Mead, RS, Rooman, I, Samra, JS, Pajic, M, Musgrove, EA, Pearson, JV, Morey, AL, Grimmond, SM, and Biankin, AV
- Abstract
Background: Pancreatic cancer is one of the most lethal and molecularly diverse malignancies. Repurposing of therapeutics that target specific molecular mechanisms in different disease types offers potential for rapid improvements in outcome. Although HER2 amplification occurs in pancreatic cancer, it is inadequately characterized to exploit the potential of anti-HER2 therapies. Methods: HER2 amplification was detected and further analyzed using multiple genomic sequencing approaches. Standardized reference laboratory assays defined HER2 amplification in a large cohort of patients (n = 469) with pancreatic ductal adenocarcinoma (PDAC). Results: An amplified inversion event (1 MB) was identified at the HER2 locus in a patient with PDAC. Using standardized laboratory assays, we established diagnostic criteria for HER2 amplification in PDAC, and observed a prevalence of 2%. Clinically, HER2- amplified PDAC was characterized by a lack of liver metastases, and a preponderance of lung and brain metastases. Excluding breast and gastric cancer, the incidence of HER2-amplified cancers in the USA is >22,000 per annum. Conclusions: HER2 amplification occurs in 2% of PDAC, and has distinct features with implications for clinical practice. The molecular heterogeneity of PDAC implies that even an incidence of 2% represents an attractive target for anti-HER2 therapies, as options for PDAC are limited. Recruiting patients based on HER2 amplification, rather than organ of origin, could make trials of anti-HER2 therapies feasible in less common cancer types. © 2013 Chou et al.; licensee BioMed Central Ltd.
- Published
- 2013
20. The histone deacetylase SIRT2 stabilizes Myc oncoproteins
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Liu, PY, Xu, N, Malyukova, A, Scarlett, CJ, Sun, YT, Zhang, XD, Ling, D, Su, SP, Nelson, CA, Chang, DK, Koach, J, Tee, AE, Haber, M, Norris, MD, Rooman, I, Toon, C, Xue, C, Cheung, B, Kumar, S, Marshall, GM, Biankin, AV, Liu, T, Liu, PY, Xu, N, Malyukova, A, Scarlett, CJ, Sun, YT, Zhang, XD, Ling, D, Su, SP, Nelson, CA, Chang, DK, Koach, J, Tee, AE, Haber, M, Norris, MD, Rooman, I, Toon, C, Xue, C, Cheung, B, Kumar, S, Marshall, GM, Biankin, AV, and Liu, T
- Published
- 2013
21. Somatic Point Mutation Calling in Low Cellularity Tumors
- Author
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Jordan, IK, Kassahn, KS, Holmes, O, Nones, K, Patch, A-M, Miller, DK, Christ, AN, Harliwong, I, Bruxner, TJ, Xu, Q, Anderson, M, Wood, S, Leonard, C, Taylor, D, Newell, F, Song, S, Idrisoglu, S, Nourse, C, Nourbakhsh, E, Manning, S, Wani, S, Steptoe, A, Pajic, M, Cowley, MJ, Pinese, M, Chang, DK, Gill, AJ, Johns, AL, Wu, J, Wilson, PJ, Fink, L, Biankin, AV, Waddell, N, Grimmond, SM, Pearson, JV, Jordan, IK, Kassahn, KS, Holmes, O, Nones, K, Patch, A-M, Miller, DK, Christ, AN, Harliwong, I, Bruxner, TJ, Xu, Q, Anderson, M, Wood, S, Leonard, C, Taylor, D, Newell, F, Song, S, Idrisoglu, S, Nourse, C, Nourbakhsh, E, Manning, S, Wani, S, Steptoe, A, Pajic, M, Cowley, MJ, Pinese, M, Chang, DK, Gill, AJ, Johns, AL, Wu, J, Wilson, PJ, Fink, L, Biankin, AV, Waddell, N, Grimmond, SM, and Pearson, JV
- Abstract
Somatic mutation calling from next-generation sequencing data remains a challenge due to the difficulties of distinguishing true somatic events from artifacts arising from PCR, sequencing errors or mis-mapping. Tumor cellularity or purity, sub-clonality and copy number changes also confound the identification of true somatic events against a background of germline variants. We have developed a heuristic strategy and software (http://www.qcmg.org/bioinformatics/qsnp/) for somatic mutation calling in samples with low tumor content and we show the superior sensitivity and precision of our approach using a previously sequenced cell line, a series of tumor/normal admixtures, and 3,253 putative somatic SNVs verified on an orthogonal platform.
- Published
- 2013
22. RON is not a prognostic marker for resectable pancreatic cancer
- Author
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Tactacan, CM, Chang, DK, Cowley, MJ, Humphrey, ES, Wu, J, Gill, AJ, Chou, A, Nones, K, Grimmond, SM, Sutherland, RL, Biankin, AV, Daly, RJ, Tactacan, CM, Chang, DK, Cowley, MJ, Humphrey, ES, Wu, J, Gill, AJ, Chou, A, Nones, K, Grimmond, SM, Sutherland, RL, Biankin, AV, and Daly, RJ
- Abstract
BACKGROUND: The receptor tyrosine kinase RON exhibits increased expression during pancreatic cancer progression and promotes migration, invasion and gemcitabine resistance of pancreatic cancer cells in experimental models. However, the prognostic significance of RON expression in pancreatic cancer is unknown. METHODS: RON expression was characterized in several large cohorts, including a prospective study, totaling 492 pancreatic cancer patients and relationships with patient outcome and clinico-pathologic variables were assessed. RESULTS: RON expression was associated with outcome in a training set, but this was not recapitulated in the validation set, nor was there any association with therapeutic responsiveness in the validation set or the prospective study. CONCLUSIONS: Although RON is implicated in pancreatic cancer progression in experimental models, and may constitute a therapeutic target, RON expression is not associated with prognosis or therapeutic responsiveness in resected pancreatic cancer.
- Published
- 2012
23. The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma
- Author
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Perez-Mancera, PA, Rust, AG, van der Weyden, L, Kristiansen, G, Li, A, Sarver, AL, Silverstein, KAT, Gruetzmann, R, Aust, D, Ruemmele, P, Knoesel, T, Herd, C, Stemple, DL, Kettleborough, R, Brosnan, JA, Morgan, R, Knight, S, Yu, J, Stegeman, S, Collier, LS, ten Hoeve, JJ, de Ridder, J, Klein, AP, Goggins, M, Hruban, RH, Chang, DK, Biankin, AV, Grimmond, SM, Wessels, LFA, Wood, SA, Iacobuzio-Donahue, CA, Pilarsky, C, Largaespada, DA, Adams, DJ, Tuveson, DA, Perez-Mancera, PA, Rust, AG, van der Weyden, L, Kristiansen, G, Li, A, Sarver, AL, Silverstein, KAT, Gruetzmann, R, Aust, D, Ruemmele, P, Knoesel, T, Herd, C, Stemple, DL, Kettleborough, R, Brosnan, JA, Morgan, R, Knight, S, Yu, J, Stegeman, S, Collier, LS, ten Hoeve, JJ, de Ridder, J, Klein, AP, Goggins, M, Hruban, RH, Chang, DK, Biankin, AV, Grimmond, SM, Wessels, LFA, Wood, SA, Iacobuzio-Donahue, CA, Pilarsky, C, Largaespada, DA, Adams, DJ, and Tuveson, DA
- Abstract
Pancreatic ductal adenocarcinoma (PDA) remains a lethal malignancy despite much progress concerning its molecular characterization. PDA tumours harbour four signature somatic mutations in addition to numerous lower frequency genetic events of uncertain significance. Here we use Sleeping Beauty (SB) transposon-mediated insertional mutagenesis in a mouse model of pancreatic ductal preneoplasia to identify genes that cooperate with oncogenic Kras(G12D) to accelerate tumorigenesis and promote progression. Our screen revealed new candidate genes for PDA and confirmed the importance of many genes and pathways previously implicated in human PDA. The most commonly mutated gene was the X-linked deubiquitinase Usp9x, which was inactivated in over 50% of the tumours. Although previous work had attributed a pro-survival role to USP9X in human neoplasia, we found instead that loss of Usp9x enhances transformation and protects pancreatic cancer cells from anoikis. Clinically, low USP9X protein and messenger RNA expression in PDA correlates with poor survival after surgery, and USP9X levels are inversely associated with metastatic burden in advanced disease. Furthermore, chromatin modulation with trichostatin A or 5-aza-2'-deoxycytidine elevates USP9X expression in human PDA cell lines, indicating a clinical approach for certain patients. The conditional deletion of Usp9x cooperated with Kras(G12D) to accelerate pancreatic tumorigenesis in mice, validating their genetic interaction. We propose that USP9X is a major tumour suppressor gene with prognostic and therapeutic relevance in PDA.
- Published
- 2012
24. Expression of S100A2 Calcium-Binding Protein Predicts Response to Pancreatectomy for Pancreatic Cancer
- Author
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Biankin, AV, Kench, JG, Colvin, EK, Segara, D, Scarlett, CJ, Nguyen, NQ, Chang, DK, Morey, AL, Lee, CS, Pinese, M, Kuo, SCL, Susanto, JM, Cosman, PH, Lindeman, GJ, Visvader, JE, Nguyen, TV, Merrett, ND, Warusavitarne, J, Musgrove, EA, Henshall, SM, Sutherland, RL, Biankin, AV, Kench, JG, Colvin, EK, Segara, D, Scarlett, CJ, Nguyen, NQ, Chang, DK, Morey, AL, Lee, CS, Pinese, M, Kuo, SCL, Susanto, JM, Cosman, PH, Lindeman, GJ, Visvader, JE, Nguyen, TV, Merrett, ND, Warusavitarne, J, Musgrove, EA, Henshall, SM, and Sutherland, RL
- Abstract
Background & Aims: Current methods of preoperative staging and predicting outcome following pancreatectomy for pancreatic cancer (PC) are inadequate. We evaluated the utility of multiple biomarkers from distinct biologic pathways as potential predictive markers of response to pancreatectomy and patient survival. Methods: We assessed the relationship of candidate biomarkers known, or suspected, to be aberrantly expressed in PC, with disease-specific survival and response to therapy in a cohort of 601 patients. Results: Of the 17 candidate biomarkers examined, only elevated expression of S100A2 was an independent predictor of survival in both the training (n = 162) and validation sets (n = 439; hazard ratio [HR], 2.19; 95% confidence interval [CI]: 1.48-3.25; P < .0001) when assessed in a multivariate model with clinical variables. Patients with high S100A2 expressing tumors had no survival benefit with pancreatectomy compared with those with locally advanced disease, whereas those without high S100A2 expression had a survival advantage of 10.6 months (19.4 vs 8.8 months, respectively) and a HR of 3.23 (95% CI: 2.39-4.33; P < .0001). Of significance, patients with S100A2-negative tumors had a significant survival benefit from pancreatectomy even in the presence of involved surgical margins (median, 15.7 months; P = .0007) or lymph node metastases (median, 17.4 months; P = .0002). Conclusions: S100A2 expression is a good predictor of response to pancreatectomy for PC and suggests that high S100A2 expression may be a marker of a metastatic phenotype. Prospective measurement of S100A2 expression in diagnostic biopsy samples has potential clinical utility as a predictive marker of response to pancreatectomy and other therapies that target locoregional disease. © 2009 AGA Institute.
- Published
- 2009
25. The Differential Diagnosis of Ritual Abuse Allegations
- Author
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Bernet, W and Chang, DK
- Abstract
Objective: Because psychiatrics do not have a consistent way to classify and define the forms of child abuse that may be mistaken for ritual abuse, the objective of this paper is to create a comprehensive differential diagnosis of allegations of ritual abuse. Method: The authors reviewed 60 articles, chapters, and books that contained allegations of ritual abuse or behaviors that might be mistaken for ritual abuse, that were made by patients or caretakers. Results: This paper clarifies the behaviors that represent or may be mistaken for ritual abuse: Cult-based ritual abuse, pseudoritualistic abuse, activities by organized satanic groups, repetitive psychopathological abuse, sexual abuse by pedophiles, child pornography portraying ritual abuse, distorted memory, false memory, false report due to a severe mental disorder, pseudologia phantastica, adolescent behavior simulating ritual abuse, epidemic hysteria, deliberate lying, and hoaxes. Conclusions: The differential diagnosis of allegations of ritual abuse is important in both clinical and forensic psychiatry. In some cases, it will not be possible to tell whether a particular allegation is factual or what the underlying mental processes are. It is important to separate the role of the mental health professional as therapist from the role as an expert witness in court.
- Published
- 1997
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26. Histomolecular phenotypes and outcome in adenocarcinoma of the ampulla of vater
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Marc D. Jones, Nigel B. Jamieson, Aldo Scarpa, Euan J. Dickson, Marina Pajic, Venessa T. Chin, Christopher J. Scarlett, Anthony J. Gill, James G. Kench, Claudio Bassi, Adnan Nagrial, R. Scott Mead, Christopher W. Toon, Amber L. Johns, Jaswinder S. Samra, Alan K. Foulis, Samantha Bersani, Andreia V. Pinho, Mohamed A. Mohamed, Karin A. Oien, Massimo Falconi, Emily K. Colvin, Nicola Sperandio, Stefano Crippa, Elizabeth A. Musgrove, David K. Chang, Jeremy L. Humphris, Mark Pinese, Robert L. Sutherland, C. Ross Carter, Vincenzo Corbo, Jianmin Wu, Colin J. McKay, Lorraine A. Chantrill, Ilse Rooman, Angela Chou, Rita T. Lawlor, Andrew V. Biankin, Mark J. Cowley, Chang, Dk, Jamieson, Nb, Johns, Al, Scarlett, Cj, Pajic, M, Chou, A, Pinese, M, Humphris, Jl, Jones, Md, Toon, C, Nagrial, Am, Chantrill, La, Chin, Vt, Pinho, Av, Rooman, I, Cowley, Mj, Wu, J, Mead, R, Colvin, Ek, Samra, J, Corbo, V, Bassi, C, Falconi, Massimo, Lawlor, Rt, Falconi, M., Crippa, Stefano, Cell Differentiation, and Laboratory for Medical and Molecular Oncology
- Subjects
Oncology ,Adult ,Male ,Cancer Research ,medicine.medical_specialty ,Ampulla of Vater ,Common Bile Duct Neoplasms ,phenotypes ,adenocarcinoma ,ampulla of vater ,Kaplan-Meier Estimate ,Keratin-20 ,Clinical decision making ,Internal medicine ,medicine ,Humans ,Aged ,Neoplasm Staging ,Homeodomain Proteins ,Mucin-2 ,business.industry ,Keratin 20 ,Keratin-7 ,Mucin-1 ,Middle Aged ,medicine.disease ,Prognosis ,Phenotype ,Immunohistochemistry ,digestive system diseases ,medicine.anatomical_structure ,multivariate analysis ,Keratin 7 ,Adenocarcinoma ,Cohort studies ,Neoplasm staging ,Female ,business ,aged, 80 and over - Abstract
Purpose Individuals with adenocarcinoma of the ampulla of Vater demonstrate a broad range of outcomes, presumably because these cancers may arise from any one of the three epithelia that converge at that location. This variability poses challenges for clinical decision making and the development of novel therapeutic strategies. Patients and Methods We assessed the potential clinical utility of histomolecular phenotypes defined using a combination of histopathology and protein expression (CDX2 and MUC1) in 208 patients from three independent cohorts who underwent surgical resection for adenocarcinoma of the ampulla of Vater. Results Histologic subtype and CDX2 and MUC1 expression were significant prognostic variables. Patients with a histomolecular pancreaticobiliary phenotype (CDX2 negative, MUC1 positive) segregated into a poor prognostic group in the training (hazard ratio [HR], 3.34; 95% CI, 1.69 to 6.62; P < .001) and both validation cohorts (HR, 5.65; 95% CI, 2.77 to 11.5; P < .001 and HR, 2.78; 95% CI, 1.25 to 7.17; P = .0119) compared with histomolecular nonpancreaticobiliary carcinomas. Further stratification by lymph node (LN) status defined three clinically relevant subgroups: one, patients with histomolecular nonpancreaticobiliary (intestinal) carcinoma without LN metastases who had an excellent prognosis; two, those with histomolecular pancreaticobiliary carcinoma with LN metastases who had a poor outcome; and three, the remainder of patients (nonpancreaticobiliary, LN positive or pancreaticobiliary, LN negative) who had an intermediate outcome. Conclusion Histopathologic and molecular criteria combine to define clinically relevant histomolecular phenotypes of adenocarcinoma of the ampulla of Vater and potentially represent distinct diseases with significant implications for current therapeutic strategies, the ability to interpret past clinical trials, and future trial design.
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- 2013
27. Subcutaneous Infliximab Concentration Thresholds for Mucosal and Transmural Healing in Patients With Crohn's Disease.
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Hong SN, Song JH, Kim SJ, Park YH, Choi CW, Kim JE, Kim ER, Chang DK, and Kim YH
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Background: Predose trough concentrations (C
trough ) of intravenous infliximab (IV-IFX) during maintenance therapy are associated with therapeutic outcomes in patients with Crohn's disease (CD). A subcutaneous formulation of infliximab (SC-IFX) has shown high Ctrough values due to its favourable pharmacokinetics., Aims: To evaluate the association of Ctrough of SC-IFX with therapeutic outcomes and the threshold of SC-IFX Ctrough for achieving mucosal healing (MH) and transmural healing (TH) in patients with CD., Methods: We performed this cross-sectional study in patients with CD who had received SC-IFX maintenance therapy for ≥ 6 months. We measured SC-IFX Ctrough immediately before SC-IFX injection. We performed ileocolonoscopy/single-balloon enteroscopy and/or magnetic resonance enterography within 3 months of SC-IFX Ctrough measurement. MH was defined as SES-CD-ulcerated surface subscore of 0. TH was defined as simplified MaRIA score of 0., Results: We enrolled 124 patients with MH in 77.9% (74/95) and TH in 36.3% (37/102). SC-IFX Ctrough was significantly higher in patients with MH (24.1 vs.16.9 μg/mL; p = 0.001) and TH (26.0 vs. 20.5 μg/mL; p = 0.007) than in those without. ROC analysis identified that the threshold of SC-IFX Ctrough for MH and TH were 17.5 and 30.3 μg/mL, respectively. Multivariate logistic regression showed that SC-IFX Ctrough was significantly associated with MH (OR 1.16; 95% CI 1.05-1.27; p = 0.002) and TH (OR 1.08; 95% CI 1.02-1.14; p = 0.005)., Conclusions: SC-IFX Ctrough was positively associated with MH (≥ 18 μg/mL) and TH (≥ 30 μg/mL) in patients with CD, which may guide treatment decisions to optimise therapeutic response in the era of treat-to-target., (© 2024 John Wiley & Sons Ltd.)- Published
- 2024
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28. Rebamipide Prevents the Hemoglobin Drop Related to Mucosal-Damaging Agents at a Level Comparable to Proton Pump Inhibitors.
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Kim JE, Lee YC, Kim TS, Kim ER, Hong SN, Kim YH, Kim K, and Chang DK
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- Humans, Retrospective Studies, Male, Female, Middle Aged, Aged, Anti-Ulcer Agents therapeutic use, Gastric Mucosa drug effects, Intestinal Mucosa drug effects, Proton Pump Inhibitors therapeutic use, Alanine analogs & derivatives, Alanine therapeutic use, Alanine pharmacology, Hemoglobins drug effects, Hemoglobins analysis, Quinolones therapeutic use, Histamine H2 Antagonists therapeutic use
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Background/aims: : The effect of proton pump inhibitors (PPIs) on the lower gastrointestinal (GI) tract is uncertain, with potential to worsen damage. This study aimed to find the best method for protecting the entire GI tract from mucosal damage., Methods: : A retrospective cohort study at Samsung Medical Center (2002-2019) included 195,817 patients prescribed GI mucosa-damaging agents. The primary goal was to assess the effectiveness of GI protective agents in preventing significant hemoglobin drops (>2 g/dL), indicating overall GI mucosal damage. Self-controlled case series and landmark analysis were used to address biases in real-world data., Results: : The incidence rate ratios for rebamipide, PPI, and histamine-2 receptor antagonist (H2RA) were 0.34, 0.33, and 0.52, respectively. Rebamipide showed a significantly lower incidence rate than H2RA and was comparable to PPIs. Landmark analysis revealed significant reductions in hemoglobin drop risk with rebamipide and H2RA, but not with PPI., Conclusions: : Rebamipide, like PPIs, was highly effective in preventing blood hemoglobin level decreases, as shown in real-world data. Rebamipide could be a comprehensive strategy for protecting the entire GI tract, especially when considering PPIs' potential side effects on the lower GI tract.
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- 2024
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29. Effectiveness of switching to subcutaneous infliximab in inflammatory bowel disease patients with inadequate biochemical response during intravenous administration.
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Lee B, Kim M, Kim ER, Hong SN, Chang DK, and Kim YH
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- Humans, Female, Male, Adult, Retrospective Studies, Injections, Subcutaneous, Middle Aged, Treatment Outcome, Gastrointestinal Agents administration & dosage, Gastrointestinal Agents therapeutic use, Feces chemistry, Drug Substitution, Infliximab administration & dosage, Infliximab therapeutic use, Infliximab pharmacokinetics, Inflammatory Bowel Diseases drug therapy, Inflammatory Bowel Diseases metabolism, C-Reactive Protein metabolism, C-Reactive Protein analysis, Administration, Intravenous, Leukocyte L1 Antigen Complex analysis
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Infliximab (IFX) has transformed the management of inflammatory bowel diseases (IBD). While intravenous (IV) IFX has been effective, a subcutaneous (SC) formulation offers advantages in convenience and cost. However, there is lack of evidence regarding the transition from IV to SC-IFX, especially for patients with inadequate responses. This study investigates the effectiveness of switching from IV to SC-IFX in patients with inadequate responses during IV maintenance therapy. A retrospective study enrolled IBD patients who transitioned to SC-IFX after demonstrating inadequate responses during IV maintenance therapy. The study collected data of demographics of patients and dose and therapies administered prior to the IV-IFX. Primary outcomes included improvements in C-reactive protein (CRP) or fecal calprotectin (FC) levels. This study evaluated the trough levels and its differences between pre- and post-switching. Among 44 patients included, 10 exhibited CRP elevation before the switch, with 6 showing normalization post-switch. Similarly, 42 patients had elevated FC levels pre-switch, with 26 experiencing reductions post-switch. Trough levels increased after the switch. However, there were no significant differences between responders and non-responders. This study is the first study to investigate the transition therapy of IV to SC-IFX in patients with inadequate response. This suggests that SC-IFX could be a viable alternative in the management of IBD. However, further research is necessary to evaluate its efficacy in a larger population of patients who exhibit inadequate responses during IV-IFX maintenance therapy., (© 2024. The Author(s).)
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- 2024
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30. nSMase2-mediated exosome secretion shapes the tumor microenvironment to immunologically support pancreatic cancer.
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Hendley AM, Ashe S, Urano A, Ng M, Phu TA, Peng XL, Luan C, Finger AM, Jang GH, Kerper NR, Berrios DI, Jin D, Lee J, Riahi IR, Gbenedio OM, Chung C, Roose JP, Yeh JJ, Gallinger S, Biankin AV, O'Kane GM, Ntranos V, Chang DK, Dawson DW, Kim GE, Weaver VM, Raffai RL, and Hebrok M
- Abstract
The pleiotropic roles of nSMase2-generated ceramide include regulation of intracellular ceramide signaling and exosome biogenesis. We investigated the effects of eliminating nSMase2 on early and advanced PDA, including its influence on the microenvironment. Employing the KPC mouse model of pancreatic cancer, we demonstrate that pancreatic epithelial nSMase2 ablation reduces neoplasia and promotes a PDA subtype switch from aggressive basal-like to classical. nSMase2 elimination prolongs survival of KPC mice, hinders vasculature development, and fosters a robust immune response. nSMase2 loss leads to recruitment of cytotoxic T cells, N1-like neutrophils, and abundant infiltration of anti-tumorigenic macrophages in the pancreatic preneoplastic microenvironment. Mechanistically, we demonstrate that nSMase2-expressing PDA cell small extracellular vesicles (sEVs) reduce survival of KPC mice; PDA cell sEVs generated independently of nSMase2 prolong survival of KPC mice and reprogram macrophages to a proinflammatory phenotype. Collectively, our study highlights previously unappreciated opposing roles for exosomes, based on biogenesis pathway, during PDA progression.
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- 2024
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31. External validation of a deep learning model for automatic segmentation of skeletal muscle and adipose tissue on abdominal CT images.
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van Dijk DPJ, Volmer LF, Brecheisen R, Martens B, Dolan RD, Bryce AS, Chang DK, McMillan DC, Stoot JHMB, West MA, Rensen SS, Dekker A, Wee L, and Olde Damink SWM
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- Humans, Male, Female, Middle Aged, Aged, Body Composition, Adipose Tissue diagnostic imaging, Radiography, Abdominal methods, Intra-Abdominal Fat diagnostic imaging, Neural Networks, Computer, Deep Learning, Tomography, X-Ray Computed methods, Muscle, Skeletal diagnostic imaging
- Abstract
Objectives: Body composition assessment using CT images at the L3-level is increasingly applied in cancer research and has been shown to be strongly associated with long-term survival. Robust high-throughput automated segmentation is key to assess large patient cohorts and to support implementation of body composition analysis into routine clinical practice. We trained and externally validated a deep learning neural network (DLNN) to automatically segment L3-CT images., Methods: Expert-drawn segmentations of visceral and subcutaneous adipose tissue (VAT/SAT) and skeletal muscle (SM) of L3-CT-images of 3187 patients undergoing abdominal surgery were used to train a DLNN. The external validation cohort was comprised of 2535 patients with abdominal cancer. DLNN performance was evaluated with (geometric) dice similarity (DS) and Lin's concordance correlation coefficient., Results: There was a strong concordance between automatic and manual segmentations with median DS for SM, VAT, and SAT of 0.97 (IQR: 0.95-0.98), 0.98 (IQR: 0.95-0.98), and 0.95 (IQR: 0.92-0.97), respectively. Concordance correlations were excellent: SM 0.964 (0.959-0.968), VAT 0.998 (0.998-0.998), and SAT 0.992 (0.991-0.993). Bland-Altman metrics indicated only small and clinically insignificant systematic offsets; SM radiodensity: 0.23 Hounsfield units (0.5%), SM: 1.26 cm2.m-2 (2.8%), VAT: -1.02 cm2.m-2 (1.7%), and SAT: 3.24 cm2.m-2 (4.6%)., Conclusion: A robustly-performing and independently externally validated DLNN for automated body composition analysis was developed., Advances in Knowledge: This DLNN was successfully trained and externally validated on several large patient cohorts. The trained algorithm could facilitate large-scale population studies and implementation of body composition analysis into clinical practice., (© The Author(s) 2024. Published by Oxford University Press on behalf of the British Institute of Radiology.)
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- 2024
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32. Histologic improvement predicts endoscopic remission in patients with ulcerative colitis.
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Kim JE, Kim M, Kim MJ, Kim ER, Hong SN, Chang DK, Ha SY, and Kim YH
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- Humans, Male, Female, Adult, Middle Aged, Treatment Outcome, Prognosis, Retrospective Studies, Severity of Illness Index, Recurrence, Colitis, Ulcerative pathology, Colonoscopy, Remission Induction
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Limited research has been performed to determine if histologic improvement serves as a prognosticator for endoscopic remission, a key therapeutic target for ulcerative colitis (UC). The primary aim of the study was to evaluate if histological activity could predict endoscopic remission in UC patients with Mayo endoscopic subscores (MES) of 0 or 1. In addition, we compared the clinical outcomes between histologic improvement group and active group. This research encompassed 492 individuals with UC with MES of 0 or 1, who underwent histological assessment as per the established protocol of Samsung Medical Center between January 2018 and December 2020. Participants were categorized into two cohorts based on the degree of histological activity: those showing histologic improvement and those with ongoing histologic activity. The endoscopic activity was assessed during follow-up, and the primary outcome was endoscopic remission according to histologic activity. Out of the total participants, endoscopic activity was scrutinized in 435 patients during the colonoscopic follow-up and in 146 during the subsequent one. The histologic improvement group at the index colonoscopy was more likely achieve endoscopic remission than the histologic active group. Clinical relapse was more likely in the histologic active group than in the histologic improvement group., (© 2024. The Author(s).)
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- 2024
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33. Integrating metabolic profiling of pancreatic juice with transcriptomic analysis of pancreatic cancer tissue identifies distinct clinical subgroups.
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Pulvirenti A, Barbagallo M, Putignano AR, Pea A, Polidori R, Upstill-Goddard R, Cortese N, Kunderfranco P, Brunelli L, De Simone G, Pastorelli R, Spaggiari P, Nappo G, Jamieson NB, Zerbi A, Chang DK, Capretti G, and Marchesi F
- Abstract
Introduction: Metabolic reprogramming is a hallmark feature of pancreatic ductal adenocarcinoma (PDAC). A pancreatic juice (PJ) metabolic signature has been reported to be prognostic of oncological outcome for PDAC. Integration of PJ profiling with transcriptomic and spatial characterization of the tumor microenvironment would help in identifying PDACs with peculiar vulnerabilities., Methods: We performed a transcriptomic analysis of 26 PDAC samples grouped into 3 metabolic clusters (M_CL) according to their PJ metabolic profile. We analyzed molecular subtypes and transcriptional differences. Validation was performed by multidimensional imaging on tumor slides., Results: Pancreatic juice metabolic profiling was associated with PDAC transcriptomic molecular subtypes (p=0.004). Tumors identified as M_CL1 exhibited a non-squamous molecular phenotype and demonstrated longer survival. Enrichment analysis revealed the upregulation of immune genes and pathways in M_CL1 samples compared to M_CL2, the group with worse prognosis, a difference confirmed by immunofluorescence on tissue slides. Enrichment analysis of 39 immune signatures by xCell confirmed decreased immune signatures in M_CL2 compared to M_CL1 and allowed a stratification of patients associated with longer survival., Discussion: PJ metabolic fingerprints reflect PDAC molecular subtypes and the immune microenvironment, confirming PJ as a promising source of biomarkers for personalized therapy., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Pulvirenti, Barbagallo, Putignano, Pea, Polidori, Upstill-Goddard, Cortese, Kunderfranco, Brunelli, De Simone, Pastorelli, Spaggiari, Nappo, Jamieson, Zerbi, Chang, Capretti and Marchesi.)
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- 2024
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34. Risk factors and management of iatrogenic colorectal perforation in diagnostic colonoscopy: a single-center cohort study.
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Kim A, Kim H, Kim ER, Kim JE, Hong SN, Chang DK, and Kim YH
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- Humans, Female, Male, Retrospective Studies, Aged, Middle Aged, Risk Factors, Aged, 80 and over, Incidence, Adult, Rectum injuries, Colon injuries, Colonoscopy adverse effects, Intestinal Perforation etiology, Iatrogenic Disease
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Background and Aims: Diagnostic colonoscopy plays a central role in colorectal cancer screening programs. We analyzed the risk factors for perforation during diagnostic colonoscopy and discussed the treatment outcomes., Methods: We performed a retrospective analysis of risk factors and treatment outcomes of perforation during 74,426 diagnostic colonoscopies between 2013 and 2018 in a tertiary hospital., Results: A total of 19 perforations were identified after 74,426 diagnostic colonoscopies or sigmoidoscopies, resulting in a standardized incidence rate of 0.025% or 2.5 per 10,000 colonoscopies. The majority (15 out of 19, 79%) were found at the sigmoid colon and recto-sigmoid junction. Perforation occurred mostly in less than 1000 cases of colonoscopy (16 out of 19, 84%). In particular, the incidence of perforation was higher in more than 200 cases undergoing slightly advanced colonoscopy rather than beginners who had just learned colonoscopy. Old age (≥ 70 years), inpatient setting, low body mass index (BMI), and sedation status were significantly associated with increased risk of perforation. Nine (47%) of the patients underwent operative treatment and ten (53%) were managed non-operatively. Patients who underwent surgery were often diagnosed with delayed or concomitant abdominal pain. Perforations of rectum tended to be successfully treated with endoscopic clipping., Conclusions: Additional precautions are required to prevent perforation in elderly patients, hospital settings, low BMI, sedated patients, or by a doctor with slight familiarity with endoscopies (but still insufficient experience). Endoscopic treatment should be actively considered if diagnosis is prompt, abdominal pain absent, and especially the rectal perforation is present.
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- 2024
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35. Disruption of the pro-oncogenic c-RAF-PDE8A complex represents a differentiated approach to treating KRAS-c-RAF dependent PDAC.
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Cooke SF, Wright TA, Sin YY, Ling J, Kyurkchieva E, Phanthaphol N, Mcskimming T, Herbert K, Rebus S, Biankin AV, Chang DK, Baillie GS, and Blair CM
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- Humans, Proto-Oncogene Proteins p21(ras) genetics, Proto-Oncogene Proteins p21(ras) metabolism, Signal Transduction, Cell Proliferation, Cell Line, Tumor, 3',5'-Cyclic-AMP Phosphodiesterases metabolism, Pancreatic Neoplasms drug therapy, Pancreatic Neoplasms genetics, Pancreatic Neoplasms metabolism, Carcinoma, Pancreatic Ductal drug therapy, Carcinoma, Pancreatic Ductal genetics, Carcinoma, Pancreatic Ductal metabolism
- Abstract
Pancreatic ductal adenocarcinoma (PDAC) is considered the third leading cause of cancer mortality in the western world, offering advanced stage patients with few viable treatment options. Consequently, there remains an urgent unmet need to develop novel therapeutic strategies that can effectively inhibit pro-oncogenic molecular targets underpinning PDACs pathogenesis and progression. One such target is c-RAF, a downstream effector of RAS that is considered essential for the oncogenic growth and survival of mutant RAS-driven cancers (including KRAS
MT PDAC). Herein, we demonstrate how a novel cell-penetrating peptide disruptor (DRx-170) of the c-RAF-PDE8A protein-protein interaction (PPI) represents a differentiated approach to exploiting the c-RAF-cAMP/PKA signaling axes and treating KRAS-c-RAF dependent PDAC. Through disrupting the c-RAF-PDE8A protein complex, DRx-170 promotes the inactivation of c-RAF through an allosteric mechanism, dependent upon inactivating PKA phosphorylation. DRx-170 inhibits cell proliferation, adhesion and migration of a KRASMT PDAC cell line (PANC1), independent of ERK1/2 activity. Moreover, combining DRx-170 with afatinib significantly enhances PANC1 growth inhibition in both 2D and 3D cellular models. DRx-170 sensitivity appears to correlate with c-RAF dependency. This proof-of-concept study supports the development of DRx-170 as a novel and differentiated strategy for targeting c-RAF activity in KRAS-c-RAF dependent PDAC., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)- Published
- 2024
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36. Clinicopathologic and Endosonographic Characteristics of Colon Subepithelial Tumors Discovered Incidentally.
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Kim A, Hong SN, Chang DK, Kim YH, Kim JE, and Kim ER
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Background/aims: Colonoscopy is commonly used for colorectal cancer screening; therefore, the detection of colon subepithelial tumors (SETs) has also increased. Several research studies have been undertaken to diagnose and treat stomach and rectal SETs. The purpose of this study was to determine a diagnostic point for colon SETs by comparing histological findings with the endoscopic characteristics of colon SETs discovered by chance., Methods: A total 194 patients underwent an endoscopic ultrasound (EUS) for suspicious colon SETs during a colonoscopy from May 2014 to December 2021. A total of 105 colon SETs, which were histologically diagnosed, were finally included. Fisher's exact test was used to determine the factors associated with malignant SETs., Results: Colon SETs were predominantly present in the right colon ( n = 73, 69.5%), particularly in the transverse colon ( n = 32, 30.5%). The majority were smaller than 10 mm ( n = 88, 83.8%), and they had hard consistencies ( n = 84, 80%) and exhibited no surface changes ( n = 96, 91.4%). Most of them were found in the submucosal layers ( n = 54, 51.4%) and had a hypoechoic pattern ( n = 56, 53.3%) in the EUS. Of the histologically confirmed cases, only three (3/105, 2.9%) were malignant. Most benign lesions were lipomas, suspected parasitic infections, or lesions caused by various inflammatory reactions, including fibrous/fibrocalcific lesions and necrotic nodules. All soft lesions were benign. Two of the three malignant lesions were adenocarcinomas, and the other was lymphoma. For the malignant SETs, there was a statistically significant alteration in the surface of the tumors ( p < 0.001), and they were located where the muscularis mucosa layer was included ( p = 0.008). The potential malignant SETs, granular cell tumors, and neuroendocrine tumors (NETs) had similar features, such as yellowish hypoechoic masses. Colon NETs were only found in the rectosigmoid junction. Parasitic infections and lesions, resulting in various inflammatory reactions, were observed as pale and hard SETs and mostly revealed as mixed echogenic masses located in the muscularis mucosa, submucosa, or multi-layers in the EUS., Conclusion: This study showed that small colon SETs were mostly benign lesions. Despite its rarity, pathological confirmation is crucial in cases where the SET has surface changes and has been located in a position where the muscularis mucosa layer was included on the EUS, due to the risk of malignancy.
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- 2024
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37. JAK/STAT3 represents a therapeutic target for colorectal cancer patients with stromal-rich tumors.
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Pennel KAF, Hatthakarnkul P, Wood CS, Lian GY, Al-Badran SSF, Quinn JA, Legrini A, Inthagard J, Alexander PG, van Wyk H, Kurniawan A, Hashmi U, Gillespie MA, Mills M, Ammar A, Hay J, Andersen D, Nixon C, Rebus S, Chang DK, Kelly C, Harkin A, Graham J, Church D, Tomlinson I, Saunders M, Iveson T, Lannagan TRM, Jackstadt R, Maka N, Horgan PG, Roxburgh CSD, Sansom OJ, McMillan DC, Steele CW, Jamieson NB, Park JH, Roseweir AK, and Edwards J
- Subjects
- Humans, Animals, Mice, Retrospective Studies, Signal Transduction, Hypoxia, Keratins metabolism, STAT3 Transcription Factor genetics, STAT3 Transcription Factor metabolism, Cell Line, Tumor, Colorectal Neoplasms drug therapy, Colorectal Neoplasms genetics, Colorectal Neoplasms metabolism
- Abstract
Colorectal cancer (CRC) is a heterogenous malignancy underpinned by dysregulation of cellular signaling pathways. Previous literature has implicated aberrant JAK/STAT3 signal transduction in the development and progression of solid tumors. In this study we investigate the effectiveness of inhibiting JAK/STAT3 in diverse CRC models, establish in which contexts high pathway expression is prognostic and perform in depth analysis underlying phenotypes. In this study we investigated the use of JAK inhibitors for anti-cancer activity in CRC cell lines, mouse model organoids and patient-derived organoids. Immunohistochemical staining of the TransSCOT clinical trial cohort, and 2 independent large retrospective CRC patient cohorts was performed to assess the prognostic value of JAK/STAT3 expression. We performed mutational profiling, bulk RNASeq and NanoString GeoMx® spatial transcriptomics to unravel the underlying biology of aberrant signaling. Inhibition of signal transduction with JAK1/2 but not JAK2/3 inhibitors reduced cell viability in CRC cell lines, mouse, and patient derived organoids (PDOs). In PDOs, reduced Ki67 expression was observed post-treatment. A highly significant association between high JAK/STAT3 expression within tumor cells and reduced cancer-specific survival in patients with high stromal invasion (TSP
high ) was identified across 3 independent CRC patient cohorts, including the TrasnSCOT clinical trial cohort. Patients with high phosphorylated STAT3 (pSTAT3) within the TSPhigh group had higher influx of CD66b + cells and higher tumoral expression of PDL1. Bulk RNAseq of full section tumors showed enrichment of NFκB signaling and hypoxia in these cases. Spatial deconvolution through GeoMx® demonstrated higher expression of checkpoint and hypoxia-associated genes in the tumor (pan-cytokeratin positive) regions, and reduced lymphocyte receptor signaling in the TME (pan-cytokeratin- and αSMA-) and αSMA (pan-cytokeratin- and αSMA +) areas. Non-classical fibroblast signatures were detected across αSMA + regions in cases with high pSTAT3. Therefore, in this study we have shown that inhibition of JAK/STAT3 represents a promising therapeutic strategy for patients with stromal-rich CRC tumors. High expression of JAK/STAT3 proteins within both tumor and stromal cells predicts poor outcomes in CRC, and aberrant signaling is associated with distinct spatially-dependant differential gene expression., (© 2024. The Author(s).)- Published
- 2024
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38. Experience of primary intestinal lymphangiectasia in adults: Twelve case series from a tertiary referral hospital.
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Na JE, Kim JE, Park S, Kim ER, Hong SN, Kim YH, and Chang DK
- Abstract
Background: While primary intestinal lymphangiectasia (PIL) is considered a rare condition, there have been several reported cases in adults. Nevertheless, the absence of clear guidance from diagnosis to treatment and prognosis poses challenges for both physicians and patients., Aim: To enhance understanding by investigating clinical presentation, diagnosis, treatment, complications, and prognoses in adult PIL cases., Methods: We enrolled adult patients diagnosed with PIL between March 2016 and September 2021. The primary outcome involved examining the diagnosis and treatment process of these patients. The secondary outcomes included identifying complications (infections, thromboembolism) and assessing prognoses (frequency of hospitalization and mortality) during the follow-up period., Results: Among the 12 included patients, peripheral edema (100%) and diarrhea (75%) were the main presenting complaints. Laboratory tests showed that all the patients exhibited symptoms of hypoalbuminemia and hypogammaglobulinemia. Radiologically, the predominant findings were edema of the small intestine (67%) and ascites (58%). The typical endoscopic finding with a snowflake appearance was observed in 75% of patients. Among the 12 patients, two responded positively to octreotide and sirolimus, and eight who could undergo maintenance therapy discontinued subsequently. Complications due to PIL led to infection in half of the patients, thromboembolism in three patients, and one death., Conclusion: PIL can be diagnosed in adults across various age groups, with different severity and treatment responses among patients, leading to diverse complications and prognoses. Consequently, tailored treatments will be necessary. We anticipate that our findings will contribute to the management of PIL, an etiology of protein-losing enteropathy., Competing Interests: Conflict-of-interest statement: The authors have no conflicts of interest relevant to this study to disclose., (©The Author(s) 2024. Published by Baishideng Publishing Group Inc. All rights reserved.)
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- 2024
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39. Time-restricted ketogenic diet in amyotrophic lateral sclerosis: a case study.
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Phillips MCL, Johnston SE, Simpson P, Chang DK, Mather D, and Dick RJ
- Abstract
Amyotrophic lateral sclerosis (ALS) is an incurable neurodegenerative disorder. The most devastating variant is bulbar-onset ALS, which portends a median survival of 24 months from the onset of symptoms. Abundant evidence indicates that neuron metabolism and mitochondrial function are impaired in ALS. Metabolic strategies, particularly fasting and ketogenic diet protocols, alter neuron metabolism and mitochondria function in a manner that may mitigate the symptoms of this disorder. We report the case of a 64-year-old man with a 21-month history of progressive, deteriorating bulbar-onset ALS, with an associated pseudobulbar affect, who implemented a time-restricted ketogenic diet (TRKD) for 18 months. During this time, he improved in ALS-related function (7% improvement from baseline), forced expiratory volume (17% improvement), forced vital capacity (13% improvement), depression (normalized), stress levels (normalized), and quality of life (19% improvement), particularly fatigue (23% improvement). His swallowing impairment and neurocognitive status remained stable. Declines were measured in physical function, maximal inspiratory pressure, and maximal expiratory pressure. Weight loss was attenuated and no significant adverse effects occurred. This case study represents the first documented occurrence of a patient with ALS managed with either a fasting or ketogenic diet protocol, co-administered as a TRKD. We measured improved or stabilized ALS-related function, forced expiratory volume, forced vital capacity, swallowing, neurocognitive status, mood, and quality of life. Measurable declines were restricted to physical function, maximal inspiratory pressure, and maximal expiratory pressure. Now over 45 months since symptom onset, our patient remains functionally independent and dedicated to his TRKD., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Phillips, Johnston, Simpson, Chang, Mather and Dick.)
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- 2024
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40. Trends in colorectal cancer incidence according to an increase in the number of colonoscopy cases in Korea.
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Kim GH, Lee YC, Kim TJ, Hong SN, Chang DK, Kim YH, Yang DH, Moon CM, Kim K, Kim HG, and Kim ER
- Abstract
Background: The incidence of colorectal cancer (CRC) and preinvasive CRC ( e.g ., early colon cancer and advanced adenoma) is gradually increasing in several countries., Aim: To evaluate the trend in incidence of CRC and preinvasive CRC according to the increase in the number of colonoscopies performed in Korea., Methods: This retrospective cohort study enrolled Korean patients from 2002 to 2020 to evaluate the incidence of CRC and preinvasive CRC, and assess the numbers of diagnostic colonoscopies and colonoscopic polypectomies. Colonoscopy-related complications by age group were also determined., Results: The incidence of CRC showed a rapid increase, then decreased after 2012 in the 50-75 year-age group. During the study period, the rate of incidence of preinvasive CRC increased at a similar level in patients under 50 and 50-75 years of age. Since 2009, the increase has been rapid, showing a pattern similar to the increase in colonoscopies. The rate of colonoscopic polypectomy in patients aged under 50 was similar to the rate in patients over 75 years of age after 2007. The rate of complications after colonoscopy and related deaths within 3 mo was high for those over 75 years of age., Conclusion: The diagnosis of preinvasive CRC increased with the increase in the number of colonoscopies performed. As the risk of colonoscopy-related hospitalization and death is high in the elderly, if early lesions at risk of developing CRC are diagnosed and treated under or at the age of 75, colonoscopy-related complications can be reduced for those aged 76 years or over., Competing Interests: Conflict-of-interest statement: All the Authors have no conflict of interest related to the manuscript., (©The Author(s) 2024. Published by Baishideng Publishing Group Inc. All rights reserved.)
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- 2024
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41. Comparison of an Endoscopic Scoring System and the Simplified Magnetic Resonance Index of Activity in Patients with Small Bowel Crohn's Disease.
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Na JE, Kim HS, Hong SN, Song KD, Kim JE, Kim ER, Kim YH, and Chang DK
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- Humans, Severity of Illness Index, Prospective Studies, Magnetic Resonance Imaging, Magnetic Resonance Spectroscopy, Crohn Disease pathology
- Abstract
Background/aims: The newly derived simplified magnetic resonance index of activity (MARIAs) has not been verified in comparison to balloon-assisted enteroscopy (BAE) for patients with small bowel Crohn's disease (CD). We studied the correlation of MARIAs with simple endoscopic scores for CD (SES-CD) of the ileum based on magnetic resonance enterography (MRE) and BAE in patients with small bowel CD., Methods: Fifty patients with small bowel CD who underwent BAE and MRE concurrently within 3 months from September 2020 to June 2021 were enrolled in the study. The primary outcome was the correlation between the active score of ileal SES-CD (ileal SES-CDa)/ileal SES-CD and MARIAs based on BAE and MRE. The cutoff value for MARIAs identifying endoscopically active/severe disease, defined as ileal SES-CDa/ileal SES-CD of 5/7 or more, was analyzed., Results: Ileal SES-CDa/ileal SES-CD and MARIAs showed strong associations (R=0.76, p<0.001; R=0.78, p<0.001). The area under the receiver operating characteristic curve of MARIAs for ileal SES-CDa ≥5 and ileal SES-CD ≥7 was 0.92 (95% confidence interval, 0.88 to 0.97) and 0.92 (95% confidence interval, 0.87 to 0.97). The cutoff value of MARIAs for detecting active/severe disease was 3. A MARIAs index value of ≥3 identified ileal SES-CDa ≥5 with a sensitivity of 85% and specificity of 87% and detected ileal SES-CD ≥7 with a sensitivity of 87% and specificity of 86%., Conclusions: This study validated the applicability of MARIAs compared to BAE-based ileal SES-CDa/SES-CD.
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- 2024
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42. Carbodiimide and Isocyanate Hydroboration by a Cyclic Carbodiphosphorane Catalyst.
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Janda BA, Tran JA, Chang DK, Nerhood GC, Maduka Ogba O, and Liberman-Martin AL
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We report hydroboration of carbodiimide and isocyanate substrates catalyzed by a cyclic carbodiphosphorane catalyst. The cyclic carbodiphosphorane outperformed the other Lewis basic carbon species tested, including other zerovalent carbon compounds, phosphorus ylides, an N-heterocyclic carbene, and an N-heterocyclic olefin. Hydroborations of seven carbodiimides and nine isocyanates were performed at room temperature to form N-boryl formamidine and N-boryl formamide products. Intermolecular competition experiments demonstrated the selective hydroboration of alkyl isocyanates over carbodiimide and ketone substrates. DFT calculations support a proposed mechanism involving activation of pinacolborane by the carbodiphosphorane catalyst, followed by hydride transfer and B-N bond formation., (© 2023 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)
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- 2024
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43. Deep learning-based optic disc classification is affected by optic-disc tilt.
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Nam Y, Kim J, Kim K, Park KA, Kang M, Cho BH, Oh SY, Kee C, Han J, Lee GI, Kang MC, Lee D, Choi Y, Yun HJ, Park H, Kim J, Cho SJ, and Chang DK
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- Male, Humans, Middle Aged, Female, Tomography, Optical Coherence methods, Optic Disk diagnostic imaging, Optic Disk pathology, Deep Learning, Eye Abnormalities pathology, Glaucoma diagnosis, Glaucoma pathology
- Abstract
We aimed to determine the effect of optic disc tilt on deep learning-based optic disc classification. A total of 2507 fundus photographs were acquired from 2236 eyes of 1809 subjects (mean age of 46 years; 53% men). Among all photographs, 1010 (40.3%) had tilted optic discs. Image annotation was performed to label pathologic changes of the optic disc (normal, glaucomatous optic disc changes, disc swelling, and disc pallor). Deep learning-based classification modeling was implemented to develop optic-disc appearance classification models with the photographs of all subjects and those with and without tilted optic discs. Regardless of deep learning algorithms, the classification models showed better overall performance when developed based on data from subjects with non-tilted discs (AUC, 0.988 ± 0.002, 0.991 ± 0.003, and 0.986 ± 0.003 for VGG16, VGG19, and DenseNet121, respectively) than when developed based on data with tilted discs (AUC, 0.924 ± 0.046, 0.928 ± 0.017, and 0.935 ± 0.008). In classification of each pathologic change, non-tilted disc models had better sensitivity and specificity than the tilted disc models. The optic disc appearance classification models developed based all-subject data demonstrated lower accuracy in patients with the appearance of tilted discs than in those with non-tilted discs. Our findings suggested the need to identify and adjust for the effect of optic disc tilt on the optic disc classification algorithm in future development., (© 2024. The Author(s).)
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- 2024
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44. Risk Prediction of Post-Endoscopic Submucosal Dissection Coagulation Syndrome.
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Kim M, Choi CW, Kim ER, Chang DK, and Hong SN
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- Humans, Male, Female, Retrospective Studies, Middle Aged, Aged, Cross-Sectional Studies, Risk Factors, Syndrome, Colorectal Neoplasms surgery, Colorectal Neoplasms pathology, Risk Assessment, Logistic Models, Prevalence, Endoscopic Mucosal Resection adverse effects, Postoperative Complications etiology, Postoperative Complications epidemiology
- Abstract
Introduction: Endoscopic submucosal dissection (ESD) has been popular worldwide to treat laterally spreading tumors and large polyps. Post-ESD coagulation syndrome (PECS) is more common than the two major ESD-related complications, perforation, and bleeding. The aim of this study was to assess the prevalence of PECS, identify the risk factors for PECS, and create a risk prediction model for PECS., Methods: Retrospective cross-sectional study analyzed a total of 986 patients who underwent colorectal ESD. Logistic regression models were used to assess risk factors with PECS. Each risk factor was scored, and the 3-step risk stratification index of prediction model was assessed., Results: The prevalence of PECS was 21.4% (95% confidence interval [CI] = 18.9-24.1%). The risk factors of PECS in the multivariate logistic regression were tumor size (+1 cm: odds ratio [OR], 1.29; 95% CI, 1.16-7.09), cecal lesion (OR, 1.96; 95% CI, 1.09-1.53), procedure time (+30 min: OR, 1.19; 95% CI, 1.02-1.39), and ESD with snaring (OR, 0.64; 95% CI, 0.43-0.95). Applying a simplified weighted scoring system based on adjusted OR increments of 1, the risk of PECS was 12.3% (95% CI, 0.3-16.0%) for the low-risk group (score ≤4) and was 36.0% (95% CI = 29.4-43.2%) for the high-risk group (score ≥8). Overall discrimination (C-statistic = 0.629; 95% CI = 0.585-0.672) and calibration (p = 0.993) of the model were moderate to good., Conclusion: PECS occurs frequently, and the prediction model can be helpful for effective treatment and prevention of PECS., (© 2024 The Author(s). Published by S. Karger AG, Basel.)
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- 2024
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45. Effect of knowledgebase transition of a clinical decision support system on medication order and alert patterns in an emergency department.
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Jung W, Yu J, Park H, Chae MK, Lee SS, Choi JS, Kang M, Chang DK, and Cha WC
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- Humans, Medication Errors, Records, Emergency Service, Hospital, Medical Order Entry Systems, Decision Support Systems, Clinical
- Abstract
A knowledgebase (KB) transition of a clinical decision support (CDS) system occurred at the study site. The transition was made from one commercial database to another, provided by a different vendor. The change was applied to all medications in the institute. The aim of this study was to analyze the effect of KB transition on medication-related orders and alert patterns in an emergency department (ED). Data of patients, medication-related orders and alerts, and physicians in the ED from January 2018 to December 2020 were analyzed in this study. A set of definitions was set to define orders, alerts, and alert overrides. Changes in order and alert patterns before and after the conversion, which took place in May 2019, were assessed. Overall, 101,450 patients visited the ED, and 1325 physicians made 829,474 prescription orders to patients during visit and at discharge. Alert rates (alert count divided by order count) for periods A and B were 12.6% and 14.1%, and override rates (alert override count divided by alert count) were 60.8% and 67.4%, respectively. Of the 296 drugs that were used more than 100 times during each period, 64.5% of the drugs had an increase in alert rate after the transition. Changes in alert rates were tested using chi-squared test and Fisher's exact test. We found that the CDS system knowledgebase transition was associated with a significant change in alert patterns at the medication level in the ED. Careful consideration is advised when such a transition is performed., (© 2023. The Author(s).)
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- 2023
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46. Weight loss from diagnosis of Crohn's disease to one year post-diagnosis results in earlier surgery.
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Kim M, Cho M, Hong S, Song JH, Kim ER, Hong SN, Chang DK, Kim YH, and Kim JE
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- Humans, Retrospective Studies, Weight Loss, Prognosis, Prospective Studies, Crohn Disease diagnosis, Crohn Disease surgery, Crohn Disease complications
- Abstract
Malnutrition might play a key role in the prognosis of patients with Crohn's disease (CD). The aim of this study was to explore the impact of weight loss from diagnosis of CD to one-year post-diagnosis on disease prognosis in terms of surgery. Patients who were diagnosed with CD at Samsung Medical Center between 1995 to 2020 were included in this study. The study defined the "group with weight loss" as patients with weight loss in one year after diagnosis and the "group without body weight loss" as patients without weight loss in one year after diagnosis. Their data such as demographics, laboratory findings, and medical interventions were collected retrospectively. The primary outcome was confirmation of the difference in the incidence of surgery associated with CD between the group with weight loss and the group without body weight loss. We further analyzed factors associated with surgery outcomes. A total of 165 patients were analyzed in this study. Forty-one patients (24.8%) had body weight loss whereas 124 patients (75.2%) had no body weight loss. Body change at one year showed no significant association with direct surgical incidence. However, the patients with weight loss tended to undergo surgery earlier than patients without body weight loss. Among factors associated with outcomes of Crohn's surgery, the albumin was the only significant factor. Patients with weight loss had no statistically significant increase in the risk of surgery than patients without weight loss, although they tended to undergo surgery earlier than patients without body weight loss. A prospective study is needed to determine serial body weight changes during follow-up for patients with CD., (© 2023. The Author(s).)
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- 2023
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47. Can balloon-assisted enteroscopy predict disease outcomes in patients with small-bowel Crohn's disease?
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Na JE, Hong SN, Kim JE, Kim ER, Kim YH, and Chang DK
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- Humans, Constriction, Pathologic etiology, Retrospective Studies, Ulcer, Crohn Disease complications, Crohn Disease diagnostic imaging, Crohn Disease surgery, Intestinal Diseases
- Abstract
There are limited studies on the endoscopic assessment of disease activity using balloon-assisted enteroscopy (BAE) and its predictive role for long-term outcomes of patients with small bowel Crohn's disease (CD). We sought to investigate the value of BAE as a predictor of long-term outcomes in patients with small-bowel CD. A total of 111 patients with small-bowel CD whose endoscopic disease activity was assessed using BAE based on the small-bowel simple endoscopic score for Crohn's disease (small-bowel SES-CD) at Samsung Medical Center were retrospectively selected from January 2014 to August 2020. The outcome was an evaluation of the risk of surgery according to a small-bowel SES-CD of 0-6 vs. ≥ 7 and endoscopic findings (presence of any ulcer and degree of stricture) using the Cox proportional hazards model. The risk of surgery was significantly increased in patients with a small-bowel SES-CD of ≥ 7 compared to a small-bowel SES-CD of 0-6 [hazard ratio (HR) 6.31; 95% confidence interval (CI) 1.48-26.91; p = 0.013]. In addition, the risk of surgery was significantly increased in patients with stenosis with "cannot be passed" compared to the cases without stenosis (HR 12.34; 95% CI 1.66-91.92; p = 0.014), whereas there was no significance in any ulcer. The present study demonstrated the role of BAE in the endoscopic assessment of disease activity and its predictive value for the risk of surgery in small-bowel CD patients. Further optimization of BAE utilization for the assessment of disease activity is warranted in clinical practice., (© 2023. BioMed Central Ltd., part of Springer Nature.)
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- 2023
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48. ReProMSig: an integrative platform for development and application of reproducible multivariable models for cancer prognosis supporting guideline-based transparent reporting.
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Zhao T, Cao L, Ji J, Chang DK, and Wu J
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- Humans, Precision Medicine, Checklist, Neoplasms diagnosis, Neoplasms genetics, Neoplasms therapy
- Abstract
Adequate reporting is essential for evaluating the performance and clinical utility of a prognostic prediction model. Previous studies indicated a prevalence of incomplete or suboptimal reporting in translational and clinical studies involving development of multivariable prediction models for prognosis, which limited the potential applications of these models. While reporting templates introduced by the established guidelines provide an invaluable framework for reporting prognostic studies uniformly, there is a widespread lack of qualified adherence, which may be due to miscellaneous challenges in manual reporting of extensive model details, especially in the era of precision medicine. Here, we present ReProMSig (Reproducible Prognosis Molecular Signature), a web-based integrative platform providing the analysis framework for development, validation and application of a multivariable prediction model for cancer prognosis, using clinicopathological features and/or molecular profiles. ReProMSig platform supports transparent reporting by presenting both methodology details and analysis results in a strictly structured reporting file, following the guideline checklist with minimal manual input needed. The generated reporting file can be published together with a developed prediction model, to allow thorough interrogation and external validation, as well as online application for prospective cases. We demonstrated the utilities of ReProMSig by development of prognostic molecular signatures for stage II and III colorectal cancer respectively, in comparison with a published signature reproduced by ReProMSig. Together, ReProMSig provides an integrated framework for development, evaluation and application of prognostic/predictive biomarkers for cancer in a more transparent and reproducible way, which would be a useful resource for health care professionals and biomedical researchers., (© The Author(s) 2023. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)
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- 2023
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49. The optimal surgery timing after stenting in colorectal cancer patients with malignant obstruction: additionally compared with emergency surgery.
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Na JE, Kim ER, Kim JE, Hong SN, Kim YH, and Chang DK
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- Humans, Retrospective Studies, Disease-Free Survival, Progression-Free Survival, Elective Surgical Procedures, Colorectal Neoplasms complications, Colorectal Neoplasms surgery
- Abstract
Background: This study aimed to determine short-term and long-term outcomes according to time intervals after stenting and compared them with those of emergency surgery (ES) in colorectal cancer (CRC) with malignant obstruction., Methods: CRC with malignant obstructions was reviewed retrospectively between January 2008 and July 2018. Of a total of 539 patients who visited the emergency room and underwent ES, 133 were enrolled in the ES group. Of a total of 567 patients who initially received stenting and subsequently underwent elective surgery, 220 were enrolled in the SEMS group. The interval between SEMS placement and elective surgery was classified as < 11 days, 11-17 days, and > 17 days., Results: For those who received SEMS (n = 220), those with a time interval of 11-17 days (n = 97) had fewer hospital days than those with a time interval of < 11 days (n = 68) (8 days vs. 15 days) and less stoma formation than those with a time interval of > 17 days (n = 55) (1.0% vs. 14.6%). Multivariable analysis revealed a decreased risk of death for the group with a time interval of 11-17 days (20.6%) compared to the ES group (31.6%) (hazard ratio: 0.48; 95% confidence interval: 0.24-0.97). Disease-free survival was comparable between the SEMS and ES groups regardless of the time interval (log-rank p = 0.52)., Conclusions: The time interval of 11-17 days after stenting to elective surgery appeared to be associated with the most favorable outcomes., (© 2023. BioMed Central Ltd., part of Springer Nature.)
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- 2023
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50. Deep learning model for distinguishing Mayo endoscopic subscore 0 and 1 in patients with ulcerative colitis.
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Kim JE, Choi YH, Lee YC, Seong G, Song JH, Kim TJ, Kim ER, Hong SN, Chang DK, Kim YH, and Shin SY
- Subjects
- Humans, Colonoscopy methods, Severity of Illness Index, Intestinal Mucosa, Colitis, Ulcerative diagnostic imaging, Deep Learning
- Abstract
The aim of this study was to address the issue of differentiating between Mayo endoscopic subscore (MES) 0 and MES 1 using a deep learning model. A dataset of 492 ulcerative colitis (UC) patients who demonstrated MES improvement between January 2018 and December 2019 at Samsung Medical Center was utilized. Specifically, two representative images of the colon and rectum were selected from each patient, resulting in a total of 984 images for analysis. The deep learning model utilized in this study consisted of a convolutional neural network (CNN)-based encoder, with two auxiliary classifiers for the colon and rectum, as well as a final MES classifier that combined image features from both inputs. In the internal test, the model achieved an F1-score of 0.92, surpassing the performance of seven novice classifiers by an average margin of 0.11, and outperforming their consensus by 0.02. The area under the receiver operating characteristic curve (AUROC) was calculated to be 0.97 when considering MES 1 as positive, with an area under the precision-recall curve (AUPRC) of 0.98. In the external test using the Hyperkvasir dataset, the model achieved an F1-score of 0.89, AUROC of 0.86, and AUPRC of 0.97. The results demonstrate that the proposed CNN-based model, which integrates image features from both the colon and rectum, exhibits superior performance in accurately discriminating between MES 0 and MES 1 in patients with UC., (© 2023. The Author(s).)
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- 2023
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